This is my input file. Can you comment if there is any bad parameter?
production run
&cntrl
imin=0, irest=1, ntx=5,
nstlim=40000000, dt=0.0005, ntc=1,
ntpr=2000, ntwx=2000, ntwr=-1000000,
ntwv=2000, ntwe=2000,
ntt=0, tempi=300.0, temp0=300.0, ntp=0, ntb=1,
cut=10, iwrap=1,
&end
The system contains 32500 atoms. I am using Amber 11 cuda serial version. I run both on GTX 580 and Tesla C2050, but the results are the same. Did I do anything wrong?
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: Dr. Vitaly Chaban [vvchaban.gmail.com]
Sent: Friday, December 28, 2012 3:50 PM
To: AMBER Mailing List
Subject: Re: [AMBER] NPT and NVE Energy
On Fri, Dec 28, 2012 at 10:06 PM, Ismail, Mohd F. <farid.ou.edu> wrote:
> Hi, I want to ask the experience users, if anyone has seen where, during
> equlibration with NPT, the energy converged, but when the simulation is
> switched to NVE, the energy drifted, linearly, either increasing or
> decreasing compare to the equilibration. Is this normal?
>
> The energy drift is linear, which makes me wonder why. If the system is
> not fully equilibrated, I expect it to be random. The change in energy is
> like 20kcal/mol for 20ns. Is this bad?
>
>
Yes, it is bad. Probably, you have specified some bad (incompatible with
NVE) parameters, which provoke energy leakage.
--
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
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Received on Sun Dec 30 2012 - 01:30:04 PST
