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Energy minimization (EM-1.mdp) stops while doing backmapping
- yogi@martini
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6 years 3 months ago - 6 years 3 months ago #7516
by yogi@martini
Energy minimization (EM-1.mdp) stops while doing backmapping was created by yogi@martini
Hello experts,
I am trying to use initram-v5.sh to get atomistic structure from CG bilayer. Here I have my own forcefield hence, I added entry in "Mapping" folder for my molecule as Name.gromos.map and accordingly added entry in that file, I have also put up my forcefield in the current directory and called it in atomistic topology
Fortunately script initram-v5.sh is working but while doing energy minimization it just stops without any error message at perticular time step. Here is last few lines:
Energy is negative, no error message, what might be happening?
please help
One more query, if I do minimization by myself using em.mdp of my own, will it wok? what are the step I needed to take care while doing minimization, because I noticed the initram-v5.sh is doing multiple minimizations. After minimization what should I do, position restrain nvt and then position restrain npt, then nvt and npt?
Any suggestion will be helpful.
Thank you
-Yogi
I am trying to use initram-v5.sh to get atomistic structure from CG bilayer. Here I have my own forcefield hence, I added entry in "Mapping" folder for my molecule as Name.gromos.map and accordingly added entry in that file, I have also put up my forcefield in the current directory and called it in atomistic topology
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
[ molecule ]
Name
[ martini ]
C1 C5 etc
[ mapping ]
gromos
[ atoms ]
1 C1 C1
2 C2 C1
3 C3 C1
Name
[ martini ]
C1 C5 etc
[ mapping ]
gromos
[ atoms ]
1 C1 C1
2 C2 C1
3 C3 C1
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
Step= 486, Dmax= 1.7e-02 nm, Epot= -8.95593e+04 Fmax= 2.17075e+04, atom= 4795
Step= 487, Dmax= 2.1e-02 nm, Epot= -8.99072e+04 Fmax= 7.50563e+03, atom= 4795
Step= 489, Dmax= 1.3e-02 nm, Epot= -8.99903e+04 Fmax= 1.00286e+04, atom= 4795
Step= 487, Dmax= 2.1e-02 nm, Epot= -8.99072e+04 Fmax= 7.50563e+03, atom= 4795
Step= 489, Dmax= 1.3e-02 nm, Epot= -8.99903e+04 Fmax= 1.00286e+04, atom= 4795
please help
One more query, if I do minimization by myself using em.mdp of my own, will it wok? what are the step I needed to take care while doing minimization, because I noticed the initram-v5.sh is doing multiple minimizations. After minimization what should I do, position restrain nvt and then position restrain npt, then nvt and npt?
Any suggestion will be helpful.
Thank you
-Yogi
Last edit: 6 years 3 months ago by yogi@martini.
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- tsjerk
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6 years 3 months ago #7520
by tsjerk
Replied by tsjerk on topic Energy minimization (EM-1.mdp) stops while doing backmapping
The halting is strange. Gromacs should give some kind of error... If you want to try doing it stepwise yourself, the first minimization is (steepest descent,) with intramolecular non-bonded interactions turned off. This is followed by normal EM, and then position-restraint NVT in cycles with increasing time steps: 0.1, 0.2, 0.5, 1.0 and 2.0 fs. The same is then repeated for NpT
Hope it helps,
T
Hope it helps,
T
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- yogi@martini
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6 years 3 months ago #7525
by yogi@martini
Replied by yogi@martini on topic Energy minimization (EM-1.mdp) stops while doing backmapping
Thanks tsjerk for the reply.
I again re-ran the initram-v5.sh on other desktop, and it ran successfully. The issue may be related to RAM of my desktop. And yes your answer clarified processes running in the initram-v5.sh
Thanks
I again re-ran the initram-v5.sh on other desktop, and it ran successfully. The issue may be related to RAM of my desktop. And yes your answer clarified processes running in the initram-v5.sh
Thanks
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