Hi Ben and fellow Amber users,
I used the 'iwrap = 1' function in my input file but still got particles moving out of the box when I looked at the .rsrt file.
My simulation box is a triclinic cell.
Is this an inevitable feature of pmemd.cuda.mpi?
Can I get the particles to stay within the simulation box without post-simulation modifications?
Or is there something wrong with the implemenation in my input file (see below).
Regards,
Adam
Input file:
20ns MD
&cntrl
imin = 0, irest = 0, ntx = 1,
ntb = 1,
cut = 9.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 0.0, temp0 = 298.0,
ntt = 1, tautp = 0.5,
nstlim = 10000000, dt = 0.002,
iwrap = 1,
ntpr = 5000, ntwx = 5000, ntwr = 1000000
/
________________________________
From: Ben Roberts <ben.roberts.geek.nz>
To: Adam Jion <adamjion.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, March 30, 2012 8:38 AM
Subject: Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi
Hi Adam,
On 30/03/2012, at 1:05 PM, Adam Jion wrote:
> I'm simulating a system using pmemd.cuda.mpi.
> However, halfway during the simulation when I looked at the .rstrt file, I noticed that some particles are moving outside the simulation box.
> I'm new to Amber, having migrated from Gromacs :-).
> Is this normal? Is there a command to translate the particles back into the box.
In general, you should be able to set "iwrap = 1" in your input file to force automatic translation of particles back into the box. Furthermore, if you need to do so after the fact, you can use ptraj or cpptraj to create a "wrapped" version of your trajectory.
Hope this helps,
Ben
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Received on Fri Mar 30 2012 - 04:30:03 PDT
