[AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded

From: Saikat Dutta chowdhury <pbr322.dutta.gmail.com>
Date: Tue, 28 May 2019 16:37:07 +0530

Respected All,
I am trying to simulate a homopolypeptide of a modified amino acid in
explicit condition.
Since the parameters for the modified amino acid is not available, I have
prepared its parameters following the GFP tutorial. After this step I have
used the frcmod and prepin files and created the following peptide
[ACE-X-X-NH2]. Here X is my modified amino acid. I have used Tip3p water
model for explicit condition.

Next I performed energy minimization in two steps.

But when I proceeded for the equilibration (with restraint), I am getting a
"vlimit exceeded" error.
I am using following for equilibration:

*Equilibration of PGU &cntrl imin=0, irest=0, ntx=1, ntb=1, iwrap=1,
cut=10.0, ntr=1, ntc=2, ntf=2,*

* tempi=0.0, temp0=10.0, ig=-1, ntt=1, nstlim=10000, dt=0.001,
ntpr=500, ntwx=500, ntwr=500, ioutfm=1 /Hold the PGU fixed10.0RES 1

The sample errors are as follows:

vlimit exceeded for step 7094; vmax = 21.7545
vlimit exceeded for step 7101; vmax = 21.0953
vlimit exceeded for step 7103; vmax = 20.2474
vlimit exceeded for step 7106; vmax = 47.7241
vlimit exceeded for step 7107; vmax = 23.1953
vlimit exceeded for step 7108; vmax = 26.3930
vlimit exceeded for step 7110; vmax = 21.7625
vlimit exceeded for step 7111; vmax = 44.0767
vlimit exceeded for step 7118; vmax = 12944.2452
vlimit exceeded for step 7119; vmax = 30.3246
vlimit exceeded for step 7120; vmax = 21.1925
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3

Looking forward to any help/suggestion.

With regards,
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
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Received on Tue May 28 2019 - 04:30:03 PDT
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