Dear Amber users:
For some research interest, I am simulating a DNA chain without net charge with GB model in Amber 9, hydrogens are added to the backbone of DNA, the parameter files were prepared for the four DNA bases with one more H, I succeeded minimizing the DNA chain with sander before running MD, while, when I run equilibration with restart file from minimization, there is problem with vlimit exceeded, the input and error message are as follows:
Equilibration.in
equilibration structure
&cntrl
imin=0,
ntc=1,ntwx=1000,
cut=15.0,igb=1,saltcon=0.2,gbsa=1,
ntpr=1000,
nstlim=20000,dt=0.001,
ntt=3,gamma_ln = 1.0,tempi=100.0,temp0=300.0,
ntx=1,irest=0,ntb=0,
nscm=1000,
&end
****************************************
NSTEP = 1000 TIME(PS) = 1.000 TEMP(K) = 209.96 PRESS = 0.0
Etot = -3620.8085 EKtot = 501.2926 EPtot = -4122.1012
BOND = 217.4105 ANGLE = 420.0829 DIHED = 601.4908
1-4 NB = 186.8149 1-4 EEL = -3357.9774 VDWAALS = -478.7169
EELEC = -897.5833 EGB = -830.1600 RESTRAINT = 0.0000
ESURF= 16.5373
------------------------------------------------------------------------------
vlimit exceeded for step 1079; vmax = 469.6312
vlimit exceeded for step 1082; vmax = 24.5541
vlimit exceeded for step 1083; vmax = 21.9756
vlimit exceeded for step 1084; vmax = 21.4498
vlimit exceeded for step 1089; vmax = 20.2899
vlimit exceeded for step 1091; vmax = 21.6526
vlimit exceeded for step 1092; vmax = 20.3968
***************************************************
This is weird for me, can anyone give me some suggestion?
Thank you very much for help in advance
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Received on Sun May 21 2006 - 06:07:08 PDT
