Thank you Justin, <br><br>It is good to know i am not alone to not understand. So I will ask to the authors the reason of this discrepancy. <br><br>Bye <br><br>SA<br><br><div class="gmail_quote">2011/3/28 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br>
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Message: 3<br>
Date: Mon, 28 Mar 2011 07:27:11 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] mathematical expression to obtain the C6 and<br>
C12 LJ terms for the GROMOSXX ff family<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:4D90708F.7000003@vt.edu">4D90708F.7000003@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
sa wrote:<br>
> Thank you Justin for your response<br>
><br>
><br>
> I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137<br>
> and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol<br>
> 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and<br>
> C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used<br>
> the following command<br>
><br>
<br>
I cannot explain this discrepancy. Going back to the actual 53A6 source<br>
(Oostenbrink et al. JCC 2004: 25: 1656-1676), the parameters in ffnonbonded.itp<br>
are correct with respect to the original force field. The fact that Poger et<br>
al. claim the parameters are the same does not make sense to me. You may wish<br>
to contact the authors of that paper directly if you have questions about<br>
reproducing their results. I also find it curious that they list their values<br>
in sigma/epsilon rather than the conventional C6/C12 used by Gromos96 force fields.<br>
<br>
-Justin<br>
<br>
> g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output<br>
><br>
> c6 = 4.66239e-03, c12 = 4.44320e-06<br>
> sigma = 0.31370, epsilon = 1.22310<br>
> Van der Waals minimum at 0.352116, V = -1.2231<br>
><br>
> Fit of Lennard Jones (12-6) to Buckingham:<br>
> A = 199065, B = 34.0796, C = 0.00466239<br>
><br>
> Back Off! I just backed up potje.xvg to ./#potje.xvg.8#<br>
><br>
> gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen)<br>
><br>
><br>
> Did I miss something ?<br>
><br>
> Thank you again for your help<br>
><br>
> SA<br>
><br>
><br>
><br>
><br>
> sa wrote:<br>
> > Dear All,<br>
> ><br>
> > I would like to compute the C6 and C12 LJ terms for the GROMOS<br>
> 53A6 ff<br>
> > for a new atom type and incorporate them in my ffnonbonded.itp. Does<br>
> > anybody know the mathematical expressions used to obtain these terms<br>
> > from a sigma (nm) and an epsilon (kj/mol) values manually.<br>
> ><br>
><br>
> g_sigeps can do this for you. Otherwise, you can convert between<br>
> the two common<br>
> forms of the Lennard-Jones equation.<br>
><br>
> -Justin<br>
><br>
> > Thank you for your help.<br>
> ><br>
> > SA<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> <<a href="http://vt.edu" target="_blank">http://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>
--<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: Mon, 28 Mar 2011 14:07:31 +0200<br>
From: sa <<a href="mailto:sagmx.mail@gmail.com">sagmx.mail@gmail.com</a>><br>
Subject: [gmx-users] Re: mathematical expression to obtain the C6 and<br>
C12 LJ terms for the GROMOSXX ff family<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<AANLkTimWtTB4V_=<a href="mailto:NgPBVP9GA4zRnAroxNH-rQT-PrE5Y@mail.gmail.com">NgPBVP9GA4zRnAroxNH-rQT-PrE5Y@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Sorry I forget to say in my previous mail that the values obtained by<br>
g_sigeps_mpi are not similar to the values given in<br>
the GROMOS53A6 ffnonbonded.itp for the OM atom.<br>
<br>
OM 8 0.000 0.000 A 0.0022619536 7.4149321e-07<br>
<br>
So your advices are welcome.<br>
<br>
SA<br>
<br>
<br>
2011/3/28 sa <<a href="mailto:sagmx.mail@gmail.com">sagmx.mail@gmail.com</a>><br>
<br>
> Thank you Justin for your response<br>
>><br>
><br>
> I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and<br>
> epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6,<br>
> 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values<br>
> given for the same in the GROMOS53A6 ffnonbonded.itp. I used the following<br>
> command<br>
><br>
> g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output<br>
><br>
> c6 = 4.66239e-03, c12 = 4.44320e-06<br>
> sigma = 0.31370, epsilon = 1.22310<br>
> Van der Waals minimum at 0.352116, V = -1.2231<br>
><br>
> Fit of Lennard Jones (12-6) to Buckingham:<br>
> A = 199065, B = 34.0796, C = 0.00466239<br>
><br>
> Back Off! I just backed up potje.xvg to ./#potje.xvg.8#<br>
><br>
> gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen)<br>
><br>
><br>
> Did I miss something ?<br>
><br>
> Thank you again for your help<br>
><br>
> SA<br>
><br>
><br>
><br>
><br>
>> sa wrote:<br>
>> > Dear All,<br>
>> ><br>
>> > I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff<br>
>> > for a new atom type and incorporate them in my ffnonbonded.itp. Does<br>
>> > anybody know the mathematical expressions used to obtain these terms<br>
>> > from a sigma (nm) and an epsilon (kj/mol) values manually.<br>
>> ><br>
>><br>
>> g_sigeps can do this for you. Otherwise, you can convert between the two<br>
>> common<br>
>> forms of the Lennard-Jones equation.<br>
>><br>
>> -Justin<br>
>><br>
>> > Thank you for your help.<br>
>> ><br>
>> > SA<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>
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Message: 5<br>
Date: Mon, 28 Mar 2011 12:37:51 +0100<br>
From: Andr? Ferreira <<a href="mailto:aff@eq.uc.pt">aff@eq.uc.pt</a>><br>
Subject: [gmx-users] No DD grid found<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:4D90730F.7060301@eq.uc.pt">4D90730F.7060301@eq.uc.pt</a>><br>
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<br>
Dear all,<br>
<br>
I am having some problems with some molecules that I am currently<br>
simulating. I got simulation box that is constituted by 100 oligomer<br>
molecules (190 atoms each), in a cubic box with 7 nm side (50K). Since<br>
the molecule is quite long I am using a rcoulomb of 2.8 nm and rvdw of<br>
3.4 nm. When I try to perform the simulation mdrun can't find DD grid<br>
for more than 48 cores, which is a huge handicap. This is the first time<br>
that I am working with longer molecules, and I never had this problem.<br>
<br>
Really appreciate the help,<br>
André<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 28 Mar 2011 23:13:04 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] converting L to D amino acid in the CHARMM<br>
force field in GROMACS where to alter dihedral<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:4D907B50.1040902@anu.edu.au">4D907B50.1040902@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 28/03/2011 8:45 PM, maria goranovic wrote:<br>
> That would mean that a new residue type will not be required? I just<br>
> need the correct input D-coordinates?<br>
<br>
Try it, before asking about it :-) I said "I suspect you do not need to<br>
change anything about the topology", but I haven't actually done<br>
anything like this ever. Topologies and code shouldn't care about<br>
chirality, so you shouldn't need to do anything other than input the<br>
configuration you want.<br>
<br>
Mark<br>
<br>
> On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
><br>
> On 26/03/2011 2:27 AM, maria goranovic wrote:<br>
>> Yes, that would be the correct way to do this. I was hoping to<br>
>> take a shorter route, and just modifying a couple of dihedrals in<br>
>> the topology files output by pdb2gmx without having to make a new<br>
>> residue. Is that not possible at all ?<br>
><br>
> Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in<br>
> a general sense. It generates a topology that matches given<br>
> coordinates, fixing a few details as directed. It will fill<br>
> valences with hydrogen atoms, generate terminal groups, organize<br>
> disulfides, and choose protonation states of titratable residues,<br>
> but it won't change geometries in the way you seem to want.<br>
><br>
> Neither does anything in the .top/.itp files stipulate the<br>
> chirality of any center (in all-atom models). Various dihedral<br>
> angles change sign with chirality, but the dihedral functions are<br>
> all symmetric about the y-axis (i.e. even). So I suspect you do<br>
> not need to change anything about the topology. Just use a<br>
> molecule builder to change the chirality of the relevant center in<br>
> the input file to pdb2gmx.<br>
><br>
> Mark<br>
><br>
<br>
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