[gmx-users] Inconsistent results in different clusters and cores

[tarak karmakar]

I am extremely sorry for spaming the mail box. It was quite
unintentionally. Believe me I was getting the following error every
time while sending the mail.

Final-Recipient: rfc822; jaanus.karo at eesti.ee
Action: failed
Status: 5.0.0
Diagnostic-Code: X-Postfix; mail forwarding loop for jaanus.karo at eesti.ee

Tarak


---------- Forwarded message ----------
From: tarak karmakar <tarak20489 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc:
Date: Fri, 17 May 2013 15:50:25 +0530
Subject: Re: [gmx-users] Inconsistent results in different clusters and cores

On Fri, May 17, 2013 at 5:36 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> On Fri, May 17, 2013 at 1:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/17/13 6:20 AM, tarak karmakar wrote:
>>
>>> I have read the 'implementation of charmm in gromacs' by bjelkmar,
>>> JCTC. There they have used following cut-offs
>>> coulombtype=PME
>>> rcoulomb=1.2
>>> vdwtype=switch
>>> rvdw=1.2
>>> rvdw-switch=1.0
>>>
>>> I am not sure about rlist.
>>>
>>>
>> It's really unnecessary to spam the list with a dozen requests that ask
>> the same question.
>>
>> By definition, with PME, rlist = rcoulomb.  For CHARMM, use rlistlong =
>> 1.4; the message that is printed below is an error that has been fixed in
>> newer versions.
>
>
> Are you sure? Looking at the logic in src/mdlib/read_ir.c, I could not see
> how Tarak's input could have led (correctly) to that note from grompp. I am
> thinking that
> https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L170
> is
> setting rlistlong = rlist, and so
> https://github.com/gromacs/gromacs/blob/release-4-5-patches/src/kernel/readir.c#L586
> gets
> double-crossed.
>
> (Note that http://redmine.gromacs.org/issues/1164 pertained to a slightly
> different issue.)
>
> Mark
> --
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