[gmx-users] Re: gmx-users Digest, Vol 85, Issue 2
Maria Hamilton
hamilton.maria39 at gmail.com
Sun May 1 18:19:17 CEST 2011
Hi Justin
If I want to have Decane.itp file in Amber forcefield for TIP4P-EW what
should I do?
Thanks
Regards
Maria
On Sun, May 1, 2011 at 6:27 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: amber force field (lina)
> 2. Re: amber force field (Justin A. Lemkul)
> 3. Re: reg error in coordinate file (Justin A. Lemkul)
> 4. Re: How to use Inflategro with different lipid types
> (Justin A. Lemkul)
> 5. Re: How to use Inflategro with different lipid types
> (Thomas Piggot)
> 6. Re: Fatal error: Attempting to read a checkpoint file of
> version 12 with code of version 4 (Faezeh Kargar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 1 May 2011 19:23:12 +0800
> From: lina <lina.lastname at gmail.com>
> Subject: Re: [gmx-users] amber force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTinZev64g49iTq2Sm4wK2Pf=XFrSGQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> In latest version of gromacs (4.5.4 or earlier)
>
> The amber force fields were provided.
>
>
> --
> Best Regards,
>
> lina
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 01 May 2011 08:59:35 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] amber force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DBD5937.1030302 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Maria Hamilton wrote:
> > Hi all friends
> >
> > If I want to use tip4pew model for water from Amber forcefield, can I
> > use itp files in PRODRG site for the other components?
> >
>
> PRODRG topologies are (supposedly) compatible with Gromos force fields, but
> TIP4P-EW is not implemented for any of these parameter sets. Any attempt
> to
> combine these would inevitably result in fatal errors from grompp about
> missing
> atomtypes. More to the point, one should never mix and match force fields.
> See, for instance, the discussion at:
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> -Justin
>
> > Thanks
> >
> > Regards
> >
> > Maria
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 01 May 2011 09:06:04 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] reg error in coordinate file
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DBD5ABC.8050704 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> vidhya sankar wrote:
> > Dear gmx-user,
> > when i run Equilibration Phase (nvt.mdp) i got
> > the .gro files as follows
> > that is co-ordinates not defined in my .gro file
> > What should i change in my mdp file in order to remove 'nan' and to
> > obtain coordinate?
>
> I doubt the problem is that simple. "Nan" means "not a number," and thus
> represents some infinite value. So either:
>
> 1. your system blew up at the last step when the .gro file was written
> 2. there is some bug that needs to be fixed
> 3. your file system had some problem writing the .gro file
>
> To address (1), check the .log file for any pertinent messages about
> instability. For (2), you'll have to at least provide your Gromacs
> version,
> input settings (.mdp file), and perhaps a description of the hardware. For
> (3),
> check your output trajectory with gmxcheck and/or watch it in VMD (or your
> favorite viewer) and if its contents are normal and the .gro file is the
> only
> aberrant output, then it's your file system's fault, no Gromacs'.
>
> <snip>
>
> > 6.56000 4.36200 12.00000
>
> For a system of just 80 atoms, this box seems extraordinarily large. Quite
> likely your system blew up.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 01 May 2011 09:10:00 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] How to use Inflategro with different lipid
> types
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DBD5BA8.9060000 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> Ioannis Beis wrote:
> > Dear gromacs users,
> >
> > I am a new user of gromacs. I am currently trying to build a large
> > bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and
> > no protein embedded in it. I have used single lipids from
> > pre-equilibrated bilayers available at Mr. Tieleman's website. The
> > distance of center of mass of neighboring lipids is 1 nm, so there are
> > small areas with overlaps. I was hoping that I would be able to inflate
> > my membrane and have the lipids totally free of overlaps using
> > Inflategro. Subsequently, I was planning to use the shrinking steps to
> > bring the membrane into physiological size. Is this strategy valid in
> > the first place? If not, I kindly ask for an alternative.
> >
> > In case this method can be used, despite "To identify the lipid species
> > their actual residue name must be given" which is mentioned in the
> > methodology, the form "INFLATEGRO bilayer.gro scaling_factor
> > lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat
> > (protein)" only allows the use of one lipid type. How is it possible to
> > run perl with all lipid types at once? I have tried performing
> > inflations using one lipid type at a time and they work. [It worths
> > mentioning that the coordinates of the rest two (uninflated) lipid types
> > slightly change without equilibration (I assume this has to do with
> > Inflategro trying to force the molecules avoid overlaps)]. But I can't
> > treat my membrane as a system that way. I have read the publication
> > introducing the methodology, but it didn't help me solve my problem.
> >
> > I would be grateful if someone could help, also taking into account that
> > I am
> > inexperienced.
> >
>
> If you want to use InflateGRO, then you'll have to modify the code to do
> so. It
> handles only one lipid type.
>
> The alternative is to use "normal" MD simulations to pack the membrane. On
> such
> approach (just thinking out loud here, so it may not work) might be to
> simulate
> your membrane (maybe without water) with some external pressure applied to
> the
> x-y plane to compress the lipids together. You may need position
> restraints on,
> i.e., the lipid headgroups in the z-dimension only during this procedure so
> the
> lipids do not simply slam into one another and distort the membrane. Once
> you've achieved a reasonable membrane, solvate and equilibrate for a longer
> period of time in the presence of solvent and absence of any restraints.
>
> -Justin
>
> > Kindest regards,
> > Yiannis
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 1 May 2011 14:41:09 +0100
> From: Thomas Piggot <t.piggot at soton.ac.uk>
> Subject: Re: [gmx-users] How to use Inflategro with different lipid
> types
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DBD62F5.9000701 at soton.ac.uk>
> Content-Type: text/plain; charset="UTF-8"; format=flowed
>
> Hi,
>
> To construct the bilayer I would just take an equilibrated POPC bilayer
> and then randomly pick lipids to change to POPE (just by a simple
> renaming of these lipids and the atom names in the headgroup) and DPPC
> (which would just require deletion of two united-atoms from the sn-2
> chains and renaming of the lipids). Then just run for an equilibration
> on the bilayer to allow the changes to take effect.
>
> There are other approaches you could take but I see this as the simplest
> solution.
>
> Cheers
>
> Tom
>
> Justin A. Lemkul wrote:
> >
> > Ioannis Beis wrote:
> >> Dear gromacs users,
> >>
> >> I am a new user of gromacs. I am currently trying to build a large
> >> bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and
> >> no protein embedded in it. I have used single lipids from
> >> pre-equilibrated bilayers available at Mr. Tieleman's website. The
> >> distance of center of mass of neighboring lipids is 1 nm, so there are
> >> small areas with overlaps. I was hoping that I would be able to inflate
> >> my membrane and have the lipids totally free of overlaps using
> >> Inflategro. Subsequently, I was planning to use the shrinking steps to
> >> bring the membrane into physiological size. Is this strategy valid in
> >> the first place? If not, I kindly ask for an alternative.
> >>
> >> In case this method can be used, despite "To identify the lipid species
> >> their actual residue name must be given" which is mentioned in the
> >> methodology, the form "INFLATEGRO bilayer.gro scaling_factor
> >> lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat
> >> (protein)" only allows the use of one lipid type. How is it possible to
> >> run perl with all lipid types at once? I have tried performing
> >> inflations using one lipid type at a time and they work. [It worths
> >> mentioning that the coordinates of the rest two (uninflated) lipid types
> >> slightly change without equilibration (I assume this has to do with
> >> Inflategro trying to force the molecules avoid overlaps)]. But I can't
> >> treat my membrane as a system that way. I have read the publication
> >> introducing the methodology, but it didn't help me solve my problem.
> >>
> >> I would be grateful if someone could help, also taking into account that
> >> I am
> >> inexperienced.
> >>
> >
> > If you want to use InflateGRO, then you'll have to modify the code to do
> so. It
> > handles only one lipid type.
> >
> > The alternative is to use "normal" MD simulations to pack the membrane.
> On such
> > approach (just thinking out loud here, so it may not work) might be to
> simulate
> > your membrane (maybe without water) with some external pressure applied
> to the
> > x-y plane to compress the lipids together. You may need position
> restraints on,
> > i.e., the lipid headgroups in the z-dimension only during this procedure
> so the
> > lipids do not simply slam into one another and distort the membrane.
> Once
> > you've achieved a reasonable membrane, solvate and equilibrate for a
> longer
> > period of time in the presence of solvent and absence of any restraints.
> >
> > -Justin
> >
> >> Kindest regards,
> >> Yiannis
> >>
> >
>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 1 May 2011 18:18:12 +0430 (IRDT)
> From: "Faezeh Kargar" <f_kargar at iasbs.ac.ir>
> Subject: Re: [gmx-users] Fatal error: Attempting to read a checkpoint
> file of version 12 with code of version 4
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <28288.85.185.211.70.1304257692.squirrel at mail.iasbs.ac.ir>
> Content-Type: text/plain; charset="utf-8"
>
>
> <html><div>
>
>
> Thank you very
> much for your reply. could you please tell me if there is any way to solve
> this problem and restart running the code?
> Karagr
>
> >
> On 30/04/2011 11:37 PM, Faezeh Kargar wrote:
> >>
> >>
> >> > On 4/30/2011 7:22 PM, Faezeh Kargar
> wrote:
> >> >>
> >> >> Dear gmx users,
> >> >>
> >> >> My code stops running because
> of electricity voltage oscillation. it
> >> >> happened for
> several times and each time I restarted running my code.
> >>
> >> but for this time with command
> >> >>
> >> >> mdrun -s topol.tpr -x
> >> >>
> traj.part0002.part0003.part0004.part0004.part0005.xtc -cpi state.cpt
> >> >> -e
> ener.part0002.part0003.part0004.part0004.part0005.edr -g
> >>
> >> md.part0002.part0003.part0004.part0004.part0005.log &
> >> >>
> >> >> I used this command before
> without any error. but now I encountered
> >> >> error like
> this:
> >> >>
> >> >>
> >> >>
> Program mdrun, VERSION 4.0.7
> >> >> Source
> >>
> >> code file: checkpoint.c, line: 565
> >> >>
> >> >> Fatal error:
> >> >> Attempting
> >> >> to read a checkpoint file of version 12 with code of
> version 4
> >> >>
> >> >> I looked at the
> file "checkpoint.c". at first the version of
> >>
> >> checkpoint file is 4 but I do not know how and why it changes.
> >> >>
> >> >
> >> > The usual reason
> for this kind of error is that you're using an old
> >> >
> version of GROMACS to access a file written by a new version. That's
> >> not
> >> > a good idea.
> >> >
> >> > Mark
> >> >
> >>
> >> Thank
> you for your reply. I just use version 4.0.7 of GROMACS and all
> >> of files are written by this version. as I said before, I
> could
> >> restart running of my codes with this command without
> any problem.
> >>
> >
> > Version 12 is that used in
> 4.5.x, so I think you are using that version.
> > Someone may have
> changed the software and not told you about it (in
> > which case,
> tell them to stop wasting people's time). Or you've migrated
> >
> files from one place to another, or something similar.
> >
> > Mark
> > --
> > gmx-users mailing list
> gmx-users at gromacs.org
> >
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please
> search the archive at
> >
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > --
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> >
> >
>
>
> --
> 83_kargar
>
> --
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