[gmx-users] gromacs.org_gmx-users Digest, Vol 121, Issue 32

Fri May 9 01:36:53 CEST 2014

Hi , i have tested the nvidia geforce gtx 760 , it works with gromacs, you have to be careful with the drivers and cuda 

Andrés Ortega 
Ing. Electrónica 
Universidad del Valle 

El 8/05/2014, a las 13:48, gromacs.org_gmx-users-request at maillist.sys.kth.se escribió:

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> Today's Topics:
> 
>   1. Re: npt dynamics generate a lot of pdb files (Mark Abraham)
>   2. Compatible GPU List (Hadi Mehrabian)
>   3. RMSD (elham tazikeh)
>   4. Re: RMSD (Justin Lemkul)
>   5. Re: Compatible GPU List (Szil?rd P?ll)
>   6. Re: Compatible GPU List (Szil?rd P?ll)
>   7. force field (elham tazikeh)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 8 May 2014 18:51:31 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] npt dynamics generate a lot of pdb files
> Message-ID:
>    <CAMNuMATG-N3Vgz1aKSYCvHsTnKexQW7ZYjrCce=631wU_eW-cQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> By modifying nstlist, you're very likely fixing a symptom, rather than
> fixing the problem.
> 
> Mark
> 
> 
> On Thu, May 8, 2014 at 6:21 PM, Natalia Alveal F. <nalveal at bio.puc.cl>wrote:
> 
>> Dear Gromacs users,
>> Reducing the nstlist value works for me.
>> 
>> Thanks a lot for yours suggestions.
>> 
>> 
>> 2014-05-06 22:47 GMT-04:00 Justin Lemkul <jalemkul at vt.edu>:
>> 
>>> 
>>> 
>>> On 5/6/14, 5:23 PM, Riccardo Concu wrote:
>>> 
>>>> Dear Natalia,
>>>> that error basicly means your system is not well equilibrated, or it is
>>>> exploading and so on. Normally, reducing the nstlist value in your mdp
>>>> file
>>>> should work.
>>> 
>>> Usually there are far more catastrophic problems than nstlist, and the
>>> only case I've found where anything improves is during EM where nstlist
>>> must be 1. Decreasing the value may work, but I would be very surprised,
>>> and ultimately there is a price to be paid in terms of performance that
>> may
>>> not be necessary.
>>> 
>>> The OP should post a full description of prior minimization and
>>> equilibration as well as the full .mdp file for the crashing run.
>> Without
>>> that information, it's totally guesswork as to what's going on.
>>> 
>>> 
>>> -Justin
>>> 
>>> --
>>> ==================================================
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>> 
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>> 
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
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>>> send a mail to gmx-users-request at gromacs.org.
>> 
>> 
>> 
>> --
>> Natalia Alveal Fuentealba
>> Ingeniera en Bioinform?tica
>> Laboratory of Membranes Proteins Structure and Signalling
>> Departamento de Fisiolog?a
>> Pontificia Universidad Cat?lica de Chile
>> Alameda 340, Santiago, Chile
>> Fono: 56-2-3542877
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
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>> posting!
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>> send a mail to gmx-users-request at gromacs.org.
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 8 May 2014 19:07:00 +0200
> From: Hadi Mehrabian <mehrabian at outlook.com>
> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Compatible GPU List
> Message-ID: <BAY406-EAS11924D44B4F090BE2BB0157AB490 at phx.gbl>
> Content-Type: text/plain; charset="us-ascii"
> 
> The list for compatible GPUs which is attached to this email is up to date? 
> 
> Newer gpus line GTX760 or GTX780 are tested?
> 
> 
> 
> Hadi
> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 8 May 2014 10:22:21 -0700
> From: elham tazikeh <elham.tazikeh at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] RMSD
> Message-ID:
>    <CAEg2dSaB-FDSWM+qnoXz8BM1SmqkfMFESDOYKjwFcKvUzpTdFA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Dear gromacs users
> 
> Can somebody tell me how to calculate the RMSD of the peptide conformation
> relative to the NMR structure?
> 
> Best wishes
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Thu, 08 May 2014 13:25:46 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] RMSD
> Message-ID: <536BBE1A.8060502 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> On 5/8/14, 1:22 PM, elham tazikeh wrote:
>> Dear gromacs users
>> 
>> Can somebody tell me how to calculate the RMSD of the peptide conformation
>> relative to the NMR structure?
> 
> g_rms with the NMR structure passed to -s.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==================================================
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Thu, 8 May 2014 20:26:02 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
>    <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Compatible GPU List
> Message-ID:
>    <CANnYEw6QgmhfuMAUPwCqzMK5MVXT4yuxv9e2ZyxbnVuMR-Kdxw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> On Thu, May 8, 2014 at 7:07 PM, Hadi Mehrabian <mehrabian at outlook.com> wrote:
>> The list for compatible GPUs which is attached to this email is up to date?
> 
> FYI: Attachments are not accepted by the list.
> 
> Anything with compute capability >=2.0 works.
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#GPU_acceleration
> 
>> Newer gpus line GTX760 or GTX780 are tested?
> 
> We don't test a particular GPU model, but an the architecture/hardware
> generation and Kepler GTX 7xx GPUs are known to work pretty well!
> 
> --
> Szil?rd
> 
>> 
>> 
>> Hadi
>> 
>> 
>> 
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Thu, 8 May 2014 20:26:02 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
>    <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Compatible GPU List
> Message-ID:
>    <CANnYEw6QgmhfuMAUPwCqzMK5MVXT4yuxv9e2ZyxbnVuMR-Kdxw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> On Thu, May 8, 2014 at 7:07 PM, Hadi Mehrabian <mehrabian at outlook.com> wrote:
>> The list for compatible GPUs which is attached to this email is up to date?
> 
> FYI: Attachments are not accepted by the list.
> 
> Anything with compute capability >=2.0 works.
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#GPU_acceleration
> 
>> Newer gpus line GTX760 or GTX780 are tested?
> 
> We don't test a particular GPU model, but an the architecture/hardware
> generation and Kepler GTX 7xx GPUs are known to work pretty well!
> 
> --
> Szil?rd
> 
>> 
>> 
>> Hadi
>> 
>> 
>> 
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> 
> 
> ------------------------------
> 
> Message: 7
> Date: Thu, 8 May 2014 11:48:05 -0700
> From: elham tazikeh <elham.tazikeh at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] force field
> Message-ID:
>    <CAEg2dSaJQWo1x7J+iyjSQ+9K=fwzjfzfExEUT22UL7sFXCkpAg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Dear friends
> who knows about force field choosing in zinc ion complex with amyloid beta
> peptide protein???
> i,m looking forward to your reply
> thank you
> 
> 
> ------------------------------
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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> 
> End of gromacs.org_gmx-users Digest, Vol 121, Issue 32
> ******************************************************