[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.

I'm sorry if this mail went to you twice. Facing lot of problems,
here, in mail delivery failure.

Thanks,
Tarak


On Fri, May 17, 2013 at 6:22 PM, tarak karmakar <tarak20489 at gmail.com> wrote:
> @ 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
>>> --
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