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Backward issues
- FPontes11
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6 months 3 days ago #9702
by FPontes11
Backward issues was created by FPontes11
Hi everyone!
I ran simulations of a complex protein-membrane system using Martini 2.2 and now I'm trying to backmap a CG structure to an all-atom model. The atomistic representation will adopt CHARMM36 as force field. It's my first time doing conversion this kind of conversion (excluding the tutorial available on website).
I'm facing some problems during the backmapping using the script initram-v5.sh. I already tried different values for the kick parameter (started from 0.05 and added 0.5 until the value 2), but my conversion always stopped at the third minimization step due an Fatal error (Too many LINCS warnings).
Someone faced similar problem before? Should I change the initial CG structure used in the conversion? I read some suggestions about change mdp parameters, but I don't know if it's the better solution. I'm using GROMACS 2016.4.
Thank you everyone for the future comments.
I ran simulations of a complex protein-membrane system using Martini 2.2 and now I'm trying to backmap a CG structure to an all-atom model. The atomistic representation will adopt CHARMM36 as force field. It's my first time doing conversion this kind of conversion (excluding the tutorial available on website).
I'm facing some problems during the backmapping using the script initram-v5.sh. I already tried different values for the kick parameter (started from 0.05 and added 0.5 until the value 2), but my conversion always stopped at the third minimization step due an Fatal error (Too many LINCS warnings).
Someone faced similar problem before? Should I change the initial CG structure used in the conversion? I read some suggestions about change mdp parameters, but I don't know if it's the better solution. I'm using GROMACS 2016.4.
Thank you everyone for the future comments.
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- vainikka
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6 months 3 days ago #9703
by vainikka
Replied by vainikka on topic Backward issues
Hi.
Three things:
1. The third minimization step is the first one that includes non-bonded interactions. You can increase the number of energy minimization steps performed in the first two steps with the flag '-em'. By default, Backward performs 500 steps, which might not be enough for your system.
2. I'm a bit puzzled by the presence of LINCS errors. Backward should by default define -DFLEXIBLE, and martinize2 (I think) should automatically write #ifdef statements that allow the user to switch to harmonic bonds during minimization. Did you use martinize, or martinize2?
3. At the end of the day, Backward is a trial-and-error approach. You should expect to have to try several times, especially in more complex cases, such as proteins.
Three things:
1. The third minimization step is the first one that includes non-bonded interactions. You can increase the number of energy minimization steps performed in the first two steps with the flag '-em'. By default, Backward performs 500 steps, which might not be enough for your system.
2. I'm a bit puzzled by the presence of LINCS errors. Backward should by default define -DFLEXIBLE, and martinize2 (I think) should automatically write #ifdef statements that allow the user to switch to harmonic bonds during minimization. Did you use martinize, or martinize2?
3. At the end of the day, Backward is a trial-and-error approach. You should expect to have to try several times, especially in more complex cases, such as proteins.
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- FPontes11
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6 months 3 days ago #9704
by FPontes11
Replied by FPontes11 on topic Backward issues
Hi Vainikka,
Thank you for your feedback. I used 'martinize' for my system.
Well, I will increase the number of EM steps.
Thank you so much.
Thank you for your feedback. I used 'martinize' for my system.
Well, I will increase the number of EM steps.
Thank you so much.
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