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Running alchemical amino acid transformation with Martini 3
- wuzhiyi
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3 years 6 months ago #8734
by wuzhiyi
Running alchemical amino acid transformation with Martini 3 was created by wuzhiyi
I’m interested in running amino acid alchemical transformation with martini3. For example to change isoleucine to valine,
I change the atom
467 SC1 189 ILE SC1 467 0.0000 72.0 SC2 0.0 72.0; H
and the bond contraint
466 467 1 0.34100 0.29200 ; ILE > VAL
However, I noticed that when I try to run the simulation with bonded-lambdas, I got the error
Fatal error:
Function type Restricted Angles does not support currentely free energy
calculations
This seems to related to the type 10 angle used which is not perturbed and it seems that having the type 10 angle alone will trigger this fatal error and one cannot run any alchemical transformation with change in bonded terms.
I change the atom
467 SC1 189 ILE SC1 467 0.0000 72.0 SC2 0.0 72.0; H
and the bond contraint
466 467 1 0.34100 0.29200 ; ILE > VAL
However, I noticed that when I try to run the simulation with bonded-lambdas, I got the error
Fatal error:
Function type Restricted Angles does not support currentely free energy
calculations
This seems to related to the type 10 angle used which is not perturbed and it seems that having the type 10 angle alone will trigger this fatal error and one cannot run any alchemical transformation with change in bonded terms.
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- riccardo
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3 years 6 months ago #8735
by riccardo
Replied by riccardo on topic Running alchemical amino acid transformation with Martini 3
True, Gromacs doesn't support free energy (FE) calculations with a few function types including the Restricted Bending (ReB) potentials.
The workaround is to substitute that potential with a classic harmonic or cosine harmonic potential (function types 1 or 2). They will be similar enough close to the equilibrium position so as to not to really make a difference to your FE calcs - see also the plots in the paper which introduces the ReBs pubs.acs.org/doi/abs/10.1021/ct400219n .
The ReBs are there for numerical stability purposes - see: pubs.acs.org/doi/abs/10.1021/ct400219n . Even without them, you should still be able to run the FE calcs; if your system is big (i.e., contained many of such ReBs), it might be that you experience a few simulation crashes, but just re-starting the simulations should do.
Hope this helps!
The workaround is to substitute that potential with a classic harmonic or cosine harmonic potential (function types 1 or 2). They will be similar enough close to the equilibrium position so as to not to really make a difference to your FE calcs - see also the plots in the paper which introduces the ReBs pubs.acs.org/doi/abs/10.1021/ct400219n .
The ReBs are there for numerical stability purposes - see: pubs.acs.org/doi/abs/10.1021/ct400219n . Even without them, you should still be able to run the FE calcs; if your system is big (i.e., contained many of such ReBs), it might be that you experience a few simulation crashes, but just re-starting the simulations should do.
Hope this helps!
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3 years 6 months ago #8736
by wuzhiyi
Replied by wuzhiyi on topic Running alchemical amino acid transformation with Martini 3
Hi riccardo，
Thank you for your reply. I have tried to change the angle type from 10 to 2. However, I noticed that I got LINC error due to probably too low the restraint strength of the SBB and BBS angle.
I'm thinking of increasing the restraint constant to a value higher than the current 5. The martini2 uses a restraint constant of 25 paired with angle type 2 but has only one pair of restraint for each residue. I wonder if you have any suggestions with regard to how high should these restraint constants be?
Thank you for your reply. I have tried to change the angle type from 10 to 2. However, I noticed that I got LINC error due to probably too low the restraint strength of the SBB and BBS angle.
I'm thinking of increasing the restraint constant to a value higher than the current 5. The martini2 uses a restraint constant of 25 paired with angle type 2 but has only one pair of restraint for each residue. I wonder if you have any suggestions with regard to how high should these restraint constants be?
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3 years 6 months ago #8737
by wuzhiyi
Replied by wuzhiyi on topic Running alchemical amino acid transformation with Martini 3
Hi riccardo，
Thank you for your reply. I have tried to substitute the SBB and BBS angle from 10 100 5 to angle type 1 or 2 and using a restraint strength of up to 25. However, it doesn't seem that the angle restraint allows a stable simulation where I always got LINC error.
Thank you for your reply. I have tried to substitute the SBB and BBS angle from 10 100 5 to angle type 1 or 2 and using a restraint strength of up to 25. However, it doesn't seem that the angle restraint allows a stable simulation where I always got LINC error.
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3 years 6 months ago #8739
by riccardo
Replied by riccardo on topic Running alchemical amino acid transformation with Martini 3
Hi wuzhiyi and sorry for the slow follow-up. How many of such ReBs were present in the itp? I was hoping it would run and just crash a few times. Is the system properly equilibrated, i.e., does it run nicely if the ReBs are in place?
Regarding the question about the force constants, I'm not sure, you could definitely try to play around with the (i.e., increase them) to see whether they help or not with the numerical instabilities.
One last option would be to lower your time step just for the free energy calculations.
Regarding the question about the force constants, I'm not sure, you could definitely try to play around with the (i.e., increase them) to see whether they help or not with the numerical instabilities.
One last option would be to lower your time step just for the free energy calculations.
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3 years 6 months ago #8740
by wuzhiyi
Replied by wuzhiyi on topic Running alchemical amino acid transformation with Martini 3
Hi riccardo，
Thank you for the help.
I'm simulating a protein with ~200 residues so around 300~400 ReBs
with the format of
2 1 3 10 100 5 ; M(1)-M(1)-N(2) SBB
1 3 4 10 100 5 ; M(1)-N(2)-N(2) BBS
If the ReBs are there the system is very stable. It seems that increasing the force constant will help. However, I have increased it to 25 and it still gives linc error after running for a while. I'm not sure if increasing it to a higher value is ok.
I'm currently using a timestep of 20fs.
Thank you for the help.
I'm simulating a protein with ~200 residues so around 300~400 ReBs
with the format of
2 1 3 10 100 5 ; M(1)-M(1)-N(2) SBB
1 3 4 10 100 5 ; M(1)-N(2)-N(2) BBS
If the ReBs are there the system is very stable. It seems that increasing the force constant will help. However, I have increased it to 25 and it still gives linc error after running for a while. I'm not sure if increasing it to a higher value is ok.
I'm currently using a timestep of 20fs.
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- riccardo
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3 years 6 months ago #8741
by riccardo
Replied by riccardo on topic Running alchemical amino acid transformation with Martini 3
Alright, that's quite a number of ReBs.
Well, what the implications of using a higher force constant for these angles are depends on what you are interested in doing with these calculations. You should try to assess the impact on the quantity you want to compute of having different force constants on those angles.
Now, one option is that you write a little script that resubmits the simulation whenever it crashes (using the Gromacs checkpoint file). Of course, this makes sense if your simulation runs for a "decent" amount of time.
Finally, as hinted at before, you could choose to lower the time step. This should improve numerical stability. In this way, you can perhaps have *numerically stable but slower* simulations. Perhaps using 15 fs or 10 fs already works for you.
Well, what the implications of using a higher force constant for these angles are depends on what you are interested in doing with these calculations. You should try to assess the impact on the quantity you want to compute of having different force constants on those angles.
Now, one option is that you write a little script that resubmits the simulation whenever it crashes (using the Gromacs checkpoint file). Of course, this makes sense if your simulation runs for a "decent" amount of time.
Finally, as hinted at before, you could choose to lower the time step. This should improve numerical stability. In this way, you can perhaps have *numerically stable but slower* simulations. Perhaps using 15 fs or 10 fs already works for you.
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3 years 6 months ago #8742
by wuzhiyi
Replied by wuzhiyi on topic Running alchemical amino acid transformation with Martini 3
Hi riccardo，
Thank you for your help.
I wonder do you know when will martini3 available? If it will take a year or two, I will try to see which of the methods can solve my question. otherwise, I will probably just use non-alchemical methods.
Thank you for your help.
I wonder do you know when will martini3 available? If it will take a year or two, I will try to see which of the methods can solve my question. otherwise, I will probably just use non-alchemical methods.
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