[gmx-users] GridMAT-MD

[David van der Spoel]

On 2015-01-09 09:44, m g wrote:
> Dear Justin,I want to use?GridMAT-MD program?for last 70 ns my simulation, wat must i do?Many thanks,Mrs. Mahdavi
>
How about using Google?

>       On Friday, January 9, 2015 11:13 AM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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>    1. Re: RDF plot with large g(r) values (Kester Wong)
>    2.  Changing number of processors after a job restart (Nash, Anthony)
>    3. Re: gromacs.org_gmx-users Digest, Vol 129, Issue 32 (asasa qsqs)
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> Message: 1
> Date: Fri, 9 Jan 2015 11:34:19 +0900
> From: Kester Wong <Kester2014 at ibs.re.kr>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] RDF plot with large g(r) values
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> Message: 2
> Date: Fri, 9 Jan 2015 07:00:34 +0000
> From: "Nash, Anthony" <a.nash at ucl.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users]  Changing number of processors after a job
>      restart
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> Hi all,
>
> This is probably quite a fundamental bit of knowledge I am missing (and struggling to find). In an effort to just get a system running rather than waiting on a queue I am considering taking my job which has already ran for 48 hours and reducing the requested number of nodes. I would use the usual -cpi ----.cpt -noappend notation in the job script to resubmit.
>
> I have a feeling though, that all manor of parallel calculations were preserved in the check point file and are loaded upon restart. Would my job reload and recalculate all the relevant cell decomposition, etc., without throwing up an error.
>
> Many thanks
> Anthony
>
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> Message: 3
> Date: Fri, 9 Jan 2015 07:42:42 +0000 (UTC)
> From: asasa qsqs <sanaz_dr_m at yahoo.com>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>      <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 129, Issue
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> Dear Justin,I want to use?GridMAT-MD program?for last 70 ns my simulation, wat must i do?Many thanks,Mrs. Mahdavi
>
>      On Friday, January 9, 2015 5:21 AM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
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> ? 1. Re: Error : Atomtype not found (Justin Lemkul)
> ? 2. rotating triclinic box (felipe zapata)
> ? 3. Re: rotating triclinic box (Tsjerk Wassenaar)
> ? 4. compiling issue (?ric Germaneau)
> ? 5. Re: compiling issue (?ric Germaneau)
> ? 6. Re: RDF plot with large g(r) values (Kester Wong)
>
>
> ----------------------------------------------------------------------
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> Message: 1
> Date: Thu, 08 Jan 2015 10:27:26 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error : Atomtype not found
> Message-ID: <54AEA1DE.6020403 at vt.edu>
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> On 1/8/15 10:14 AM, protim chakraborti wrote:
>> Respected Dr. Lemkul
>> Thanks for the suggestion. I have checked the ffnonbonded.itp and found
>> that copper is entered out there in the following form and format
>>
>> ; Ions and noble gases (useful for tutorials)
>> Cu2+? ? 29? ? ? 63.54600? ? ? ? 2.00? ? A? ? ? 2.08470e-01? ? 4.76976e+00
>> Ar? ? ? 18? ? ? 39.94800? ? ? ? 0.00? ? A? ? ? 3.41000e-01? ? 2.74580e-02
>>
>> would this be not be suffice or i need to add Cu separately? or may be I
>> have to run starting from pdb2gmx itself!
>>
>
> Those parameters are not CHARMM parameters.? They appear to have been copied
> over from OPLS-AA, which had several ions removed due to unknown origins (as was
> Ar).? Do not use these parameters for a CHARMM simulation.? I recommend that
> they be removed entirely, as we did with our CHARMM36 port.
>
> -Justin
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se