Dear Amber users
I am simulating DNA in a solvent. After thorough minimization, I
heated up the system to 298K keeping the DNA restrained and thereafter
performed NPT at 298K keeping the restraints on. However, the system
showed a SHAKE error saying "SHAKE cannot be accomplished". So I read
out the last few frames just before the error and using VMD saw that a
C-H bond of one molecule of the solvent is stretched too much. When I
repeated the simulation, the error occured again, this time for a
different solent molecule and a N-H bond. During this entire procedure
i was using dt=0.002.
I repeated the entire procedure with dt=0.001 and went through the
entire minimization, NVT heating and NPT equilibration without any
problem. However after that when I got back to NPT with dt=0.002, the
SHAKE error occured.
Here's my input for md
&cntrl
imin = 0, ntx = 7, irest = 1,
ntpr = 1000, ntwx = 1000, ntwe = 0,
ntc = 2, ntf = 2,iwrap = 1,nstlim = 500000, dt =0.002,
tempi=298.0, temp0 = 298.0, ntt =1, tautp =2.0,
cut = 15.0, ntb = 2,ntp = 1,taup = 2.0,pres0 = 1.0
&end
Need help to know what is going wrong with my system.
Thanks in advance
--
Debostuti Ghosh Dastidar
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Received on Thu Jan 17 2013 - 03:00:04 PST
