AMBER Archive (2008)

Subject: AMBER: temperature error in md calculation

From: Catein Catherine (
Date: Wed Nov 05 2008 - 02:11:41 CST

Dear All,
I am working on a system with my own designed force field parameters for a linear pt-c7-n7 system, I determined that force field based on gaff force field and modify some of them to fit my own project. I redefined atom pt, c7, n7 in frcmod file as follows:
pt 195.09 1.00 atomic mass of pt
c7 12.01 0.360 gaff c1 (sp C)
n7 14.01 0.530 gaff n2 (aliphatic sp2 with two connected atoms)
pt-c7 366.0 2.042 based on x-ray
n7-c7 366.0 1.13 based on x-ray
pt-c7-n7 42.000 180.0 based on x-ray
pt 4.88 0.4 literature
c7 1.9080 0.0860 same as gaff c1 (cp C)
n7 1.8240 0.1700 same as gaff n1 (OPLS)
However, i found the following error message everything I run the min and md.
For the, I used.
imin=1, maxcyc=500000, ncyc=40000, ntr=0, nmropt=0,
cut=16, ntb=0, igb=1,
The error message before final results were listed in the out file is as follows:
....Restarted due to Linmin failure...
***Repeated Linmin Failure***
For, I used
imin=0, saltconc=0.3
nstlim=20000, dt=0.002, ntc=1, ntr=0, nmropt=0
ntpr=100, ntwx=100,
cut=16, ntb=0, igb=1,
ntt=3, gamma_ln=1.0,
tempi=300.0, temp0=300.0,
However, the temperature rise significantly during the md simulation
NSTEP=0, TEMP(K)=308.74
NSTEP=100, TEMP(K)=1317.96
NSTEP=200, TEMP(K)=2242.74
finally, error message likes
vlimit exceeded for step .....
structure distorted,
Etot = *****
Would you please kindly help if I have done something obviously wrong here that lead to the error message above? Please kindly help. Many thanks
Best regards,
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