[gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 1
kamakshi sikka
kamakshi.sikka at gmail.com
Wed Jun 1 08:02:32 CEST 2016
Dear Mark,
If adding ions is not an issue, can you please help me in solving this
problem.
Regards
Kamakshi Sikka
On Wed, Jun 1, 2016 at 10:30 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Error while re-compiling Gromacs 5.1.2 with GPU and gcc
> 5.3.1 (Diogo Martins de S?)
> 2. Re: Error while re-compiling Gromacs 5.1.2 with GPU and gcc
> 5.3.1 (Mark Abraham)
> 3. Re: Error while re-compiling Gromacs 5.1.2 with GPU and gcc
> 5.3.1 (Mark Abraham)
> 4. Error while generating ions.tpr file (kamakshi sikka)
> 5. Re: Error while generating ions.tpr file (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 31 May 2016 19:25:32 -0300
> From: Diogo Martins de S? <sadiogo at mol.bio.br>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with
> GPU and gcc 5.3.1
> Message-ID: <1223361464733532 at web24g.yandex.ru>
> Content-Type: text/plain; charset="us-ascii"
>
> An HTML attachment was scrubbed...
> URL: <
> http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20160531/ec5ee4df/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Tue, 31 May 2016 22:46:57 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with
> GPU and gcc 5.3.1
> Message-ID:
> <CAMNuMARC9WahukHjxkG+agepPvfrhPMi8xJc6HTg=
> 0hFD-YcdA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Either approach can work, but you could have tried your command before
> emailing :-)
>
> Mark
>
> On Wed, 1 Jun 2016 00:35 Diogo Martins de S? <sadiogo at mol.bio.br> wrote:
>
> > Hi Mark and Szilard,
> >
> > Thanks for all the help. Just to make sure I understood, I should run
> > cmake like this:
> >
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=on
> > -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda-7.5
> > -DCMAKE_C_FLAGS="-D_FORCE_INLINES"
> >
> > or should I try to modify a CMakefile.txt or Makefile? If so, which? I've
> > been looking around but can't seem to find the correct file to modify.
> >
> > Best regards,
> > Diogo
> >
> >
> > From: Mark Abraham <mark.j.abraham at ...
> > <
> http://gmane.org/get-address.php?address=mark.j.abraham%2dRe5JQEeQqe8AvxtiuMwx3w%40public.gmane.org
> >
> > >
> >
> > Subject: Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU
> > and gcc 5.3.1
> > <
> http://news.gmane.org/find-root.php?message_id=CAMNuMAR25zQe6exe%2bn4NL%2dPkm%3dxcmQn%5fSuv0fS4LncdPEGyP%2bQ%40mail.gmail.com
> >
> > Newsgroups: gmane.science.biology.gromacs.user
> > <http://news.gmane.org/gmane.science.biology.gromacs.user>
> > Date: 2016-05-31 21:16:07 GMT (41 minutes ago)
> >
> > Hi,
> >
> > That's the standard content of CUDA - that deliberate compiler error has
> to
> > be suppressed (per the link in the original post) if you want to use a
> > different compiler.
> >
> > The issue here is that the version of the C standard library that ships
> on
> > the operating system has a new feature that interacts poorly with
> versions
> > of CUDA that pre-dated it. Using a compatible compiler doesn't help, if
> it
> > shares that standard library. To fix, as Szilard tried to suggest, you
> can
> > use
> >
> > cmake -DCMAKE_C_FLAGS="-D_FORCE_INLINES"
> >
> > which avoids the problematic code path. The irritating part about trying
> to
> > consider a workaround for GROMACS is that memcpy is supposed to be
> defined
> > by string.h, so it is somehow inconsistent that it is not defined...
> >
> > Mark
> >
> > --
> > 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: 3
> Date: Tue, 31 May 2016 22:46:57 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with
> GPU and gcc 5.3.1
> Message-ID:
> <CAMNuMARC9WahukHjxkG+agepPvfrhPMi8xJc6HTg=
> 0hFD-YcdA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Either approach can work, but you could have tried your command before
> emailing :-)
>
> Mark
>
> On Wed, 1 Jun 2016 00:35 Diogo Martins de S? <sadiogo at mol.bio.br> wrote:
>
> > Hi Mark and Szilard,
> >
> > Thanks for all the help. Just to make sure I understood, I should run
> > cmake like this:
> >
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=on
> > -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda-7.5
> > -DCMAKE_C_FLAGS="-D_FORCE_INLINES"
> >
> > or should I try to modify a CMakefile.txt or Makefile? If so, which? I've
> > been looking around but can't seem to find the correct file to modify.
> >
> > Best regards,
> > Diogo
> >
> >
> > From: Mark Abraham <mark.j.abraham at ...
> > <
> http://gmane.org/get-address.php?address=mark.j.abraham%2dRe5JQEeQqe8AvxtiuMwx3w%40public.gmane.org
> >
> > >
> >
> > Subject: Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU
> > and gcc 5.3.1
> > <
> http://news.gmane.org/find-root.php?message_id=CAMNuMAR25zQe6exe%2bn4NL%2dPkm%3dxcmQn%5fSuv0fS4LncdPEGyP%2bQ%40mail.gmail.com
> >
> > Newsgroups: gmane.science.biology.gromacs.user
> > <http://news.gmane.org/gmane.science.biology.gromacs.user>
> > Date: 2016-05-31 21:16:07 GMT (41 minutes ago)
> >
> > Hi,
> >
> > That's the standard content of CUDA - that deliberate compiler error has
> to
> > be suppressed (per the link in the original post) if you want to use a
> > different compiler.
> >
> > The issue here is that the version of the C standard library that ships
> on
> > the operating system has a new feature that interacts poorly with
> versions
> > of CUDA that pre-dated it. Using a compatible compiler doesn't help, if
> it
> > shares that standard library. To fix, as Szilard tried to suggest, you
> can
> > use
> >
> > cmake -DCMAKE_C_FLAGS="-D_FORCE_INLINES"
> >
> > which avoids the problematic code path. The irritating part about trying
> to
> > consider a workaround for GROMACS is that memcpy is supposed to be
> defined
> > by string.h, so it is somehow inconsistent that it is not defined...
> >
> > Mark
> >
> > --
> > 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: Wed, 1 Jun 2016 10:26:35 +0530
> From: kamakshi sikka <kamakshi.sikka at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Error while generating ions.tpr file
> Message-ID:
> <CALuDt+E9_QuHwyuqDe+g5SZR4-aX7GxXj5xsmS_OH-Cg=
> pD12g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
> I am doing mixed lipid bilayer simulation with a peptide. This bilayer
> membranewas built by Charmm Gui. Afterwards, I oriented the peptide on the
> top of the bilayer and then saved the peptide+membrane complex file. Then ,
> I am trying to add ions into the system by giving the command mentioned
> below.But, this is giving an error. This membrane already has 'SOD'
> ions in it. Is it creating a problem while adding CL ions into the system?
> Please help.
>
> *COMMAND:*
> gmx grompp -f ions.mdp -c complex_new.pdb -p topol.top -o ions.tpr
>
>
> NOTE 1 [file ions.mdp, line 17]:
> ions.mdp did not specify a value for the .mdp option "cutoff-scheme".
> Probably it was first intended for use with GROMACS before 4.6. In 4.6,
> the Verlet scheme was introduced, but the group scheme was still the
> default. The default is now the Verlet scheme, so you will observe
> different behaviour.
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#
>
> NOTE 2 [file ions.mdp]:
> With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> that with the Verlet scheme, nstlist has no effect on the accuracy of
> your simulation.
>
> Setting the LD random seed to 2538245621
> Generated 73900 of the 73920 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 47534 of the 73920 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 3 bonded neighbours molecule type 'POPS'
> Excluding 3 bonded neighbours molecule type 'POPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'SOD'
>
> NOTE 3 [file topol.top, line 2253]:
> System has non-zero total charge: 5.000001
> Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> for discussion on how close it should be to an integer.
>
>
>
>
> ERROR 1 [file topol.top, line 2253]:
> ERROR: The cut-off length is longer than half the shortest box vector or
> longer than the smallest box diagonal element. Increase the box size or
> decrease rlist.
>
>
> Removing all charge groups because cutoff-scheme=Verlet
>
> There were 3 notes
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.2
> Source code file:
> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/grompp.c, line: 1723
>
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> Regards
> Kamakshi Sikka
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 01 Jun 2016 05:00:14 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error while generating ions.tpr file
> Message-ID:
> <CAMNuMAR_yj0r+WMWjhVMfbn246qesD3vp4MiUZouLzK=
> FiqgAg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> The text of the error has nothing to do with the ions you may or may not
> need to add. Please read more closely.
>
> Mark
>
> On Wed, 1 Jun 2016 06:57 kamakshi sikka <kamakshi.sikka at gmail.com> wrote:
>
> > Hello,
> >
> > I am doing mixed lipid bilayer simulation with a peptide. This bilayer
> > membranewas built by Charmm Gui. Afterwards, I oriented the peptide on
> the
> > top of the bilayer and then saved the peptide+membrane complex file.
> Then ,
> > I am trying to add ions into the system by giving the command mentioned
> > below.But, this is giving an error. This membrane already has 'SOD'
> > ions in it. Is it creating a problem while adding CL ions into the
> system?
> > Please help.
> >
> > *COMMAND:*
> > gmx grompp -f ions.mdp -c complex_new.pdb -p topol.top -o ions.tpr
> >
> >
> > NOTE 1 [file ions.mdp, line 17]:
> > ions.mdp did not specify a value for the .mdp option "cutoff-scheme".
> > Probably it was first intended for use with GROMACS before 4.6. In 4.6,
> > the Verlet scheme was introduced, but the group scheme was still the
> > default. The default is now the Verlet scheme, so you will observe
> > different behaviour.
> >
> >
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#
> >
> > NOTE 2 [file ions.mdp]:
> > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> > that with the Verlet scheme, nstlist has no effect on the accuracy of
> > your simulation.
> >
> > Setting the LD random seed to 2538245621
> > Generated 73900 of the 73920 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 1
> > Generated 47534 of the 73920 1-4 parameter combinations
> > Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> > Excluding 3 bonded neighbours molecule type 'POPS'
> > Excluding 3 bonded neighbours molecule type 'POPC'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> > Excluding 1 bonded neighbours molecule type 'SOD'
> >
> > NOTE 3 [file topol.top, line 2253]:
> > System has non-zero total charge: 5.000001
> > Total charge should normally be an integer. See
> > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > for discussion on how close it should be to an integer.
> >
> >
> >
> >
> > ERROR 1 [file topol.top, line 2253]:
> > ERROR: The cut-off length is longer than half the shortest box vector
> or
> > longer than the smallest box diagonal element. Increase the box size or
> > decrease rlist.
> >
> >
> > Removing all charge groups because cutoff-scheme=Verlet
> >
> > There were 3 notes
> >
> > -------------------------------------------------------
> > Program gmx, VERSION 5.0.2
> > Source code file:
> > /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/grompp.c, line:
> 1723
> >
> > Fatal error:
> > There was 1 error in input file(s)
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> > Regards
> > Kamakshi Sikka
> > --
> > 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.
> >
>
>
> ------------------------------
>
> --
> 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.
>
> End of gromacs.org_gmx-users Digest, Vol 146, Issue 1
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