Dear Dr. Case,
Thanks so much for your response. I wanted to send this earlier but figured I'd do a little more troubleshooting first. Your suspicion looks to be correct, as I tried a simulation without shake and did not get the large temperature spike as before. I did get some +/- 30K fluctuations near the beginning (even with a time step of 0.1 fs) but I presume this is due to the fact that the system was equilibrated with shake turned on?
To minimize temperature fluctuations I suppose one can carry out heating and volume equilibration followed by short production runs from different random seeds all with shake turned off. The runs can then be restarted with shake turned on. This option still yields a slight temperature discrepancy (quick drop of ~10K followed by steady convergence back to 300K). Is this just an unavoidable consequence of switching shake on?
I see that the randomization procedure for pmemd is defined in dynamics.F90 under vrand_set_velocities. Are you suggesting something should be changed in this procedure in order to account for shake?
Very best wishes,
Andrew
From: David A Case [david.case.rutgers.edu]
Sent: Monday, October 05, 2015 2:17 AM
To: AMBER Mailing List
Cc: amber-developers.ambermd.org
Subject: Re: [AMBER] problem with randomizing velocities
On Fri, Oct 02, 2015, Kalenkiewicz, Andrew (NIH/NICHD) [F] wrote:
>
> I am trying to start an accelerated MD simulation from an equilibrated
> system using a random seed (ig=-1) for the velocities, but for some
> reason there is a large temperature spike at the beginning of my
> simulation when I use the following input file:
>
>
> The temperature starts at ~430K, drops to around 270K, and then
> equilibrates to 300K. But according to the manual:
I suspect that the velocity randomization procedure doesn't properly recognize
the fact that bonds to hydrogen are being shaken. Try a short test simulation
without shake to see if you get good initial temperatures.
cc-ing to the Amber developers' list, since this is arguably something that
ought to be fixed. I think(?) there is code in libsff that addresses this,
but that doesn't help much for pmemd users. (Also worth checking mdgx....)
Volunteers are welcome...this is how you get established in a community.
My start in Amber was to volunteer to add second derivative code. I
polished up that code so faithfully, that now I am the ruler of the
Queen's Navy....
....dac
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Received on Thu Oct 15 2015 - 09:00:03 PDT
