I ran the check command, and no bad overlaps were found. The trajectory has the same coordinates as the .prmcrd file, which gives a realistic number when used with the default imin.
-Aaron van Dyne
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Thursday, August 08, 2013 11:27 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Trajectory post-processing
Hi,
On Thu, Aug 8, 2013 at 8:39 AM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu> wrote:
> AMBER has now been updated on the supercomputer, but I am still having the same problem.
Did you ever run the 'check' command in cpptraj/ptraj to look for bad
overlaps in the trajectory that is giving you the large VDW energy?
> On Tue, Aug 6, 2013 at 2:50 PM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu> wrote:
>> The outputted energies always have a van der Waals contribution that is on the order of 10^16.
> This indicates you have a clash somewhere in your trajectory file. Use
> the 'check' command in cpptraj or ptraj to see if there are any bad
> overlaps.
-Dan
>
> -Aaron van Dyne
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: Tuesday, August 06, 2013 8:13 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Trajectory post-processing
>
> On Tue, Aug 6, 2013 at 5:59 PM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu>wrote:
>
>> I am using Amber 12. I do not know which bug fixes have been applied (I am
>> running on the University of Pittsburgh Department of Computational and
>> Systems Biology computing cluster. I would imagine all the appropriate bug
>> fixes have been applied).
>>
>
> You can find out with the command
>
> $AMBERHOME/update_amber --version
>
> The assumption that supercomputers keep their installations up-to-date is
> rarely a good one. Since they are not regular users, they probably update
> only when requested.
>
> You can use the command:
>
> $AMBERHOME/update_amber --check
>
> to see if there are available updates.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Aug 08 2013 - 10:00:03 PDT
