Re: [AMBER] NaN error in .rst files

From: peker milas <>
Date: Mon, 24 Jan 2011 21:30:03 -0800

Than you Ross for your quick reply.

First thing to say, i am not using this flag. But as far as i know in
the manual it says that flag/option doesn't has no effect on either
force or energy calculations. That is why i didn't use it. I can turn
it on and check if same problem appears. But at the same time, i am
just in the middle of a long calculation, so then another question
appears in my mind. If i continue with iwrap flag/option, should i
expect any important difference in the simulation results ? You
definitely know much more than me about amber, can you tell me if it
is safe ?


On Mon, Jan 24, 2011 at 7:54 PM, Ross Walker <> wrote:
> Hi Peter,
> Before you check into this any further can I just confirm that you have
> iwrap=1 set in the &cntrl namelist. If not then this is the problem and it
> is a pmemd / sander issue, completely unrelated to cuda. It will, in
> principal go away if we move to netcdf restart files.
> If you can confirm this only occurs with PMEMD.cuda and you have iwrap=1 set
> then it warrants investigating and the next step will be to see if anyone
> has seen this problem on any of the Tesla cards or it is confined to GTX
> series cards.
> All the best
> Ross
>> -----Original Message-----
>> From: peker milas []
>> Sent: Monday, January 24, 2011 2:42 PM
>> To: AMBER Mailing List
>> Subject: [AMBER] NaN error in .rst files
>> Dear Amber coders/users
>> We had a discussion about this problem couple days ago. Briefly at
>> some point of simulations pmemd.cuda creates NaN s in the restart
>> files. Then the next step of simulation messes up. This is sort of a
>> problem which happens in totally random way. As some users already
>> pointed out, part of it can be related with heating problem because
>> GTX 470/480 cards were not designed for this kind of intense
>> calculations.  Although i totally agree with this, i couldn't find an
>> easy way of observing this behavior. In fact there is only nvidia-smi
>> command which shows me the current state of the card (like its
>> temperature, etc...). So i really want to go little bit deep with this
>> problem and i would like to know if anybody knows a good indicator for
>> checking cards behavior in detail. It can be a command or any sort
>> additional package/program for monitoring it.
>> Any help will be appreciated
>> regards
>> peker milas
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Received on Mon Jan 24 2011 - 22:00:04 PST
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