An update on the above inquiry.
I did try cpptraj.MPI functionality and realized that it has not been implemented yet for nativecontact analysis. I appreciate any other ideas to speed up this work or possible optimizations to my input file.
Thank you and wish you all a happy new year!!
_______________________________
Senal Liyanage
Doctoral Student
Department of Chemistry
Mississippi State, MS 39762-9573
P: 662.694.9005
________________________________
From: Delwakkada Liyanage, Senal Dinuka
Sent: Friday, December 22, 2023 2:41 PM
To: AMBER.ambermd.org <amber.ambermd.org>
Subject: nativecontact analysis speedup suggestion
Dear AMBER users,
I am trying to monitor the penetration of an ionic liquid into the bilayer and vice versa. I have already obtained density profiles and trying to obtain a contact pdb with beta values using the nativecontact analysis.
Following is the command I am using.
# 12/18/23 17:11:51
# Args: -p ../../../popc-choline_octanoate.parm7
# Loaded topologies:
# ../../../popc-choline_octanoate.parm7
trajin popc-choline_octanoate-prod-imaged-traj1.crd
nativecontacts :PA,OL :U01,U04 byresidue writecontacts nc.dat resout cres.dat out nc.all.res.dat savenonnative nncontactpdb nncontact.pdb
go
quit
I have used a 7-angstrom cutoff to capture the relevant interactions, and this took me almost 5 days to compute. I am thinking of using cpptraj.MPI functionality to speed up.
I would like to know any ideas or concerns about my approach.
Thank you,
_______________________________
Senal Liyanage
Doctoral Student
Department of Chemistry
Mississippi State, MS 39762-9573
P: 662.694.9005
_______________________________________________
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Received on Sun Dec 31 2023 - 11:00:02 PST
