Dear Amber Users,
Could you be so kind as to help me in the following situation:
I solvated some peptide in water by AMBER 8 solvatebox command, performed minimixation and equilibration (1 ns) in the NVT-ensemble at 298 K. Then, I performed eqilibration in the NPT ensemble at 1 atm for rather long time (1 ns). Now I want to use the box obtained in NVT simulations at 305 K. However, when I run such simulation Amber crashes without giving any error message except for the batch system message like that below:
The output (if any) follows:
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_14987: p4_error: : 1
Is it possible to use NPT-simulated box in the NVT-simulations in Amber? Could the use of IWRAP option during NPT simulations help? Can long equlibration times in NVT and NPT simulations play its role in the situation above?
I would be grateful for any help.
Thanks in advance,
Sergey
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Received on Thu Dec 22 2005 - 06:53:00 PST
