[gmx-users] Gromacs says that may GeForce 9800gt is incompatible any, help?
Justin Lemkul
jalemkul at vt.edu
Fri Sep 25 23:51:28 CEST 2015
Please heed this:
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
On 9/25/15 5:46 PM, Juliano Braz Carregal wrote:
> Do you know wich version of gromacs works with this gpu?the page of gromacs says
> that 9800gt is compatible,but unfortunaly its not true.
Presumably you're referring to
http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM which
is when the only acceleration was provided via OpenMM. That information is
outdated by several years. Moreover, OpenMM (at the time) only supported
implicit solvent runs with extremely limited features. You can get version 4.5
(again, way outdated) and OpenMM-2.0 (if that's even available any more, current
version is 6.2!) and try to run some limited types of simulations. But the
better bet is to get newer hardware and use modern software.
-Justin
> Thank you
>
> Em 25/09/2015 5:44 PM, gromacs.org_gmx-users-request at maillist.sys.kth.se escreveu:
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> Today's Topics:
>
> 1. Gromacs says that may GeForce 9800gt is incompatible any
> help? (Juliano Braz Carregal)
> 2. Re: Gromacs says that may GeForce 9800gt is incompatible any
> help? (Repic Matej)
> 3. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)
> 4. Re: GROMACS with AMBER heme parameters (Justin Lemkul)
> 5. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)
> 6. Re: GROMACS with AMBER heme parameters (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 25 Sep 2015 15:46:29 -0300
> From: Juliano Braz Carregal <julianocarregal at hotmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Gromacs says that may GeForce 9800gt is
> incompatible any help?
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> ------------------------------
>
> Message: 2
> Date: Fri, 25 Sep 2015 19:15:43 +0000
> From: Repic Matej <matej.repic at epfl.ch>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Gromacs says that may GeForce 9800gt is
> incompatible any help?
> Message-ID: <D22B692A.12714%matej.repic at epfl.ch>
> Content-Type: text/plain; charset="Windows-1252"
>
> Unfortunately, it is incompatible. 9800GT has compute capability 1.1, but
> gromacs needs 2.0 or higher. The oldest compatible cards are GTX 4xx series
> from 2010, but 9800GT is from 2008.
>
> Best,
> ------------------------------------------------------
> Dr. Matej Repic
> Ecole Polytechnique F?d?rale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC ? LCBC
> BCH 4108
> CH - 1015 Lausanne
> ------------------------------------------------------
>
> From:
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se>>
> on behalf of Juliano Braz Carregal
> <julianocarregal at hotmail.com<mailto:julianocarregal at hotmail.com>>
> Reply-To: "gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>"
> <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
> Date: Friday, September 25, 2015 at 20:46
> To:
> "gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>"
> <gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>>
> Subject: [gmx-users] Gromacs says that may GeForce 9800gt is incompatible
> any help?
>
>
> Gromacs 5 says that may GeForce 9800gt is incompatible any help?
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 25 Sep 2015 20:22:54 +0000
> From: Ebert Maximilian <m.ebert at umontreal.ca>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
> Message-ID: <5EF0A589-8604-438C-90ED-55ECB9FC21CE at umontreal.ca>
> Content-Type: text/plain; charset="us-ascii"
>
> Since the heme definition in AMBER uses GAFF atom types how do I get the
> GAFF FF to work in GROMACS? I would need all the bonded and non bonded
> definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
>
> Max
>
> > On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> >
> > On 9/25/15 1:32 PM, Ebert Maximilian wrote:
> >> Hi there,
> >>
> >> I am trying to simulate a heme containing protein. I found AMBER heme
> >> parameters in the mol2 and frcmod file format. I know that I can generate
> >> .itp files containing the parameters, which I can later add to my .top file.
> >> However, it would be much easier to use pdb2gmx directly without stripping
> >> the heme and the cysteine binding the heme and later manually add it
> again. I
> >> added the cysteine to the standard amber force field. However, before adding
> >> the heme manually I wanted to know if there is a way to load an itp file
> >> while executing pdb2gmx?
> >>
> >
> > pdb2gmx does not need .itp information. grompp does. Add the parameters
> to ffbonded.itp or ffnonbonded.itp as needed.
> >
> >> How would you add the information from the cysteine in mol2 format and the
> >> heme in mol2/frcmod format to amber in gromacs?
> >>
> >
> > Charges and connectivity go in the .rtp entry. Heme ligation by His and
> Cys is already supported via specbond.dat.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > 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!
> >
> > * 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: 4
> Date: Fri, 25 Sep 2015 16:25:20 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
> Message-ID: <5605ADB0.4040608 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/25/15 4:22 PM, Ebert Maximilian wrote:
> > Since the heme definition in AMBER uses GAFF atom types how do I get the
> GAFF FF to work in GROMACS? I would need all the bonded and non bonded
> definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
> >
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> -Justin
>
> > Max
> >
> >> On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>
> >> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
> >>> Hi there,
> >>>
> >>> I am trying to simulate a heme containing protein. I found AMBER heme
> >>> parameters in the mol2 and frcmod file format. I know that I can generate
> >>> .itp files containing the parameters, which I can later add to my .top
> file.
> >>> However, it would be much easier to use pdb2gmx directly without stripping
> >>> the heme and the cysteine binding the heme and later manually add it
> again. I
> >>> added the cysteine to the standard amber force field. However, before
> adding
> >>> the heme manually I wanted to know if there is a way to load an itp file
> >>> while executing pdb2gmx?
> >>>
> >>
> >> pdb2gmx does not need .itp information. grompp does. Add the
> parameters to ffbonded.itp or ffnonbonded.itp as needed.
> >>
> >>> How would you add the information from the cysteine in mol2 format and the
> >>> heme in mol2/frcmod format to amber in gromacs?
> >>>
> >>
> >> Charges and connectivity go in the .rtp entry. Heme ligation by His and
> Cys is already supported via specbond.dat.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> 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!
> >>
> >> * 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.
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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: Fri, 25 Sep 2015 20:40:19 +0000
> From: Ebert Maximilian <m.ebert at umontreal.ca>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
> Message-ID: <911260F5-AC7D-4111-BFC6-4C8C97923E44 at umontreal.ca>
> Content-Type: text/plain; charset="us-ascii"
>
> I read that and this is the way I added the cysteine to AMBER which connects
> to the heme. Now I am adding the heme but the FF definition for bonds,
> angles, etc are all in lower case for the GAFF FF. From you answer I guess I
> need to add these lower case atom types and the bonds, angles, etc
> definition from the GAFF FF to the AMBER FF manually.
>
> Not much fun but I will share the work here in the end. Maybe this will help
> people who want to simulate heme containing proteins in GROMACS and
> AMBER99SB-ILDN.
>
> Have a good weekend,
> Max
>
>
> On Sep 25, 2015, at 4:25 PM, Justin Lemkul
> <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 9/25/15 4:22 PM, Ebert Maximilian wrote:
> Since the heme definition in AMBER uses GAFF atom types how do I get the
> GAFF FF to work in GROMACS? I would need all the bonded and non bonded
> definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
>
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> -Justin
>
> Max
>
> On Sep 25, 2015, at 1:36 PM, Justin Lemkul
> <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
> Hi there,
>
> I am trying to simulate a heme containing protein. I found AMBER heme
> parameters in the mol2 and frcmod file format. I know that I can generate
> .itp files containing the parameters, which I can later add to my .top file.
> However, it would be much easier to use pdb2gmx directly without stripping
> the heme and the cysteine binding the heme and later manually add it again. I
> added the cysteine to the standard amber force field. However, before adding
> the heme manually I wanted to know if there is a way to load an itp file
> while executing pdb2gmx?
>
>
> pdb2gmx does not need .itp information. grompp does. Add the parameters to
> ffbonded.itp or ffnonbonded.itp as needed.
>
> How would you add the information from the cysteine in mol2 format and the
> heme in mol2/frcmod format to amber in gromacs?
>
>
> Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys
> is already supported via specbond.dat.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu<mailto: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!
>
> * 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.
>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu<mailto: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!
>
> * 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<mailto:gmx-users-request at gromacs.org>.
>
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 25 Sep 2015 16:43:32 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
> Message-ID: <5605B1F4.4050807 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/25/15 4:40 PM, Ebert Maximilian wrote:
> > I read that and this is the way I added the cysteine to AMBER which
> connects to the heme. Now I am adding the heme but the FF definition for
> bonds, angles, etc are all in lower case for the GAFF FF. From you answer I
> guess I need to add these lower case atom types and the bonds, angles, etc
> definition from the GAFF FF to the AMBER FF manually.
> >
>
> Indeed, which is what steps 3 and 4 tell you. Adding a residue is simple, but
> if that residue involves modifications to the force field, then there is more
> work to be done.
>
> -Justin
>
> > Not much fun but I will share the work here in the end. Maybe this will
> help people who want to simulate heme containing proteins in GROMACS and
> AMBER99SB-ILDN.
> >
> > Have a good weekend,
> > Max
> >
> >
> > On Sep 25, 2015, at 4:25 PM, Justin Lemkul
> <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > On 9/25/15 4:22 PM, Ebert Maximilian wrote:
> > Since the heme definition in AMBER uses GAFF atom types how do I get the
> GAFF FF to work in GROMACS? I would need all the bonded and non bonded
> definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
> >
> >
> >
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> >
> > -Justin
> >
> > Max
> >
> > On Sep 25, 2015, at 1:36 PM, Justin Lemkul
> <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > On 9/25/15 1:32 PM, Ebert Maximilian wrote:
> > Hi there,
> >
> > I am trying to simulate a heme containing protein. I found AMBER heme
> > parameters in the mol2 and frcmod file format. I know that I can generate
> > .itp files containing the parameters, which I can later add to my .top file.
> > However, it would be much easier to use pdb2gmx directly without stripping
> > the heme and the cysteine binding the heme and later manually add it again. I
> > added the cysteine to the standard amber force field. However, before adding
> > the heme manually I wanted to know if there is a way to load an itp file
> > while executing pdb2gmx?
> >
> >
> > pdb2gmx does not need .itp information. grompp does. Add the parameters
> to ffbonded.itp or ffnonbonded.itp as needed.
> >
> > How would you add the information from the cysteine in mol2 format and the
> > heme in mol2/frcmod format to amber in gromacs?
> >
> >
> > Charges and connectivity go in the .rtp entry. Heme ligation by His and
> Cys is already supported via specbond.dat.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> >
> jalemkul at outerbanks.umaryland.edu<mailto: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!
> >
> > * 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.
> >
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> >
> jalemkul at outerbanks.umaryland.edu<mailto: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!
> >
> > * 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<mailto:gmx-users-request at gromacs.org>.
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 137, Issue 137
> *******************************************************
>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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