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