[gmx-users] LINCS warnings at high temperature md run
chris.neale at alum.utoronto.ca
Tue Aug 9 21:35:26 CEST 2016
Try adding "lincs-order = 6" to your mdp file.
The following settings don't give me lincs warnings at 500 K, though I presume that the lincs-order is the essential part.
constraints = all-bonds
lincs-iter = 1
lincs-order = 6
constraint_algorithm = lincs
dt = 0.002
integrator = sd
tc_grps = System
tau_t = 1.0
ld_seed = -1
failing that, post your full .mdp file.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sidong Tu <sidongt at g.clemson.edu>
Sent: 09 August 2016 14:49:03
To: gromacs.org_gmx-users at maillist.sys.kth.se
Cc: Chandan K Choudhury
Subject: [gmx-users] LINCS warnings at high temperature md run
I was trying to simulate lysozyme and polymer in water model tip3p using
charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU and
the system size was about 60,000 atoms. I have done equilibrium with
Berendsen(B) and Parrinello-Rahman(PR), and then md. The thermal coupling I
used was v-rescale.
I always got a LINCS warning and my job stopped during the md. Here's the
parameter I have used:
Stage Position_Constraint Pcoupl gen_vel LINCS dt
1 Protein & polymer B yes all bonds 0.002
2 Protein B yes all bonds
3 None B yes all bonds
4 None PR no all bonds
5 None PR no h bonds
At stage 5, the md run stopped at 149 steps and showed relative constraint
deviation after LINCS.
I have searched for this warning and there is an explanation that it might
be introduced by the bad equilibrium. Then I added a equilibrium stage with
Berendsen pressure coupling after stage 3 with LINCS constraints of h bonds
for 50,000 steps without position constraints.
This time there was still warings with LINCS and it stopped at step 79026
Step 79026, time 158.052 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 15.598468, max 1553.834961 (between atoms 15966 and 15968)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
15941 15943 40.7 0.2082 0.1109 0.1111
15945 15946 75.6 0.2551 7.7014 0.1111
15945 15947 90.0 0.2299 4.2042 0.1111
15949 15950 67.8 0.1543 0.1150 0.1111
15949 15951 86.2 0.1658 8.9758 0.1111
15966 15967 90.0 0.1111 0.2587 0.1111
15966 15968 143.1 0.1111 172.7422 0.1111
15970 15971 90.0 0.1111 0.1405 0.1111
Wrote pdb files with previous and current coordinates
The simulation worked well with dt=0.001 without LINCS. But I still want to
find if there is a way to simulate at high temperature(500K) with dt=0.002
so that I can use less steps?
Department of Materials Science and Engineering
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