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Backmapping a big trajectory
- z.sichaib
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5 years 6 months ago #7819
by z.sichaib
Backmapping a big trajectory was created by z.sichaib
Dear Martini users,
I was running several MD simulations of a protein embedded in a membrane, containing POPC, POPE & CHOL molecules, using Martini FF.
In order to do a deep analysis of my system (i.e. analyzing the interactions between the Protein and CHOL), I was trying to backmap a part of the trajectory using initram.
For example, let's say I would like to backmap 6000 confirmations from the trajectory. To do so, I extracted the conformations in separate PDB files and I was applying the following loop:
import os
for fileNum in range(0,6001):
os.system("./initram-v5.sh -f mdmerged_frame" + str(fileNum) + ".gro -o mdmerged_aa_frame" + str(fileNum) + ".gro -to amber -p topol.top")
When I run this script on a supercomputer/ a big machine, it generated output files for ~2h and then it stopped. But when I check the status of the job, this latter appears to be running.
The IT service couldn't understand the problem. Now I'm thinking maybe the scripts (backward and initram) can't be run automatically on a big series of files? Or maybe there is a problem with my code. I tried several things but still can't fix the problem.
I would like to know if anyone tried to backmapy a hole/big part of a trajectory. If so I would be very grateful for the suggestions on how they did it.
I will also appreciate your comments regarding the loop that I'm using or if you have any other alternative that I can try.
I thanks everyone very much for the help!
Zeineb
I was running several MD simulations of a protein embedded in a membrane, containing POPC, POPE & CHOL molecules, using Martini FF.
In order to do a deep analysis of my system (i.e. analyzing the interactions between the Protein and CHOL), I was trying to backmap a part of the trajectory using initram.
For example, let's say I would like to backmap 6000 confirmations from the trajectory. To do so, I extracted the conformations in separate PDB files and I was applying the following loop:
import os
for fileNum in range(0,6001):
os.system("./initram-v5.sh -f mdmerged_frame" + str(fileNum) + ".gro -o mdmerged_aa_frame" + str(fileNum) + ".gro -to amber -p topol.top")
When I run this script on a supercomputer/ a big machine, it generated output files for ~2h and then it stopped. But when I check the status of the job, this latter appears to be running.
The IT service couldn't understand the problem. Now I'm thinking maybe the scripts (backward and initram) can't be run automatically on a big series of files? Or maybe there is a problem with my code. I tried several things but still can't fix the problem.
I would like to know if anyone tried to backmapy a hole/big part of a trajectory. If so I would be very grateful for the suggestions on how they did it.
I will also appreciate your comments regarding the loop that I'm using or if you have any other alternative that I can try.
I thanks everyone very much for the help!
Zeineb
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- riccardo
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5 years 6 months ago #7823
by riccardo
Replied by riccardo on topic Backmapping a big trajectory
Hi Zeineb,
Your approach sounds reasonable. Did you check whether your loop works for only the first 2 frames? So, for something like:
Your approach sounds reasonable. Did you check whether your loop works for only the first 2 frames? So, for something like:
for fileNum in range(0,2):Please Log in or Create an account to join the conversation.
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