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

[tarak karmakar]

@ Justin and Mark,

Do you have any idea about the rlist used by Bjelkmar et. al.
'Implementation of charmm in gromacs'? I see, they have performed
their simulations in gromacs-4.1 version. I'm not sure about whether
in that version the problem persisted or not.

Tarak

On Fri, May 17, 2013 at 5:42 PM, tarak karmakar <tarak20489 at gmail.com> wrote:
> 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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists