RE: [gmx-users] Viscosity using periodic perturbation method

Hi, Yes, you can use NPT, the code takes care of this properly. Strictly speaking it might be incorrect, but since pressure scaling is usually less than 1% it will not affect your results significantly. Berk. Date: Mon, 25 May 2009 15:19:10 -0700 From: yson...@asu.edu To: gmx-users@gromacs.org

Re: Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Hi Nehme, > Also, in our zinc finger models, the zinc plays a structural role and it is > not implicated in DNA recognition. Furthermore, I will read your paper and > the references. I looked in the Literature and from NMR studies/X-ray and MD > done on zinc fingers containing a zinc ion coordinat

[gmx-users] Re: oplsaa parametrization

Dear Rosa, here goes my little contribution to try to help you: http://acpypi.googlecode.com. For me, no doubt that antechamber is the best tool for getting the topological information about small molecules (pls, read the wikis in ACPYPI pages to know more). The module to generate OPLS/AA is still

[gmx-users] Lennard-Jones 9-6 potential problems

Hi everyone! Have anyone used the Lennard-Jones 9-6 potential for coarse-grained models? when I use it, I get a very different result from that is got from the same Lennard-Jones 9-6 potential formed a potential table,the latter's results are comparable to the experiments. when I use LJ-9-6

[gmx-users] Re: Dynamics with DNA

Hey Tanos, You must read some papers but my recommendations are: GMX 4.0.5 and AMBER99SB forcefield. Look at http://acpypi.googlecode.comwhere you can find info about how to add amber forcefield to GMX. Cheers, Alan Subject: [gmx-users] Dynamics with DNA > > Hi folks ! > Does someone knows

Re: [gmx-users] Lennard-Jones 9-6 potential problems

zhangjianguo2002 wrote: Hi everyone! Have anyone used the Lennard-Jones 9-6 potential for coarse-grained models? when I use it, I get a very different result from that is got from the same Lennard-Jones 9-6 potential formed a potential table,the latter's results are comparable to the expe

RE: [gmx-users] Lennard-Jones 9-6 potential problems

Hi, I forgot about this feature. Your problem is indeed that you used comb-rule=1, you have to use 2 or 3 to make this work. And indeed you should use user tables filled with the 9-6 potential. Gromacs could actually easily support p-6 tables with any value for p, by storing p in the tpr file an

[gmx-users] constant term in dihedral potential function

Dear all, I included the following dihedral potential function in a topology: V(phi2) = -5.865 + 7.470 [1+cos(phi2-180°)] + 3.99 [1+cos(2 phi2)] + 1.1 [1+cos(3 phi2-180°)] The problem is about representing the constant term -5.865. Using equation 4.61 (Gromacs 4.0 manual): V(phi) = k * (1 + c

RE: [gmx-users] constant term in dihedral potential function

Hi, I don't know how you currently supply your dihedral (multiple periodic dihedral terms?). But you can supply the whole potential, including the constant term, using a Ryckaert-Bellemans dihedral. The manual gives some conversion formulas. Berk > From: a.ku...@herts.ac.uk > To: gmx-users@gr

[gmx-users] Normal Mode Analysis

Hi, I'm quite a new user of gromacs. I want to do an all-atom normal mode analysis of a small protein in water. As a result I would like to have the hessian matrix in a readable format, that I can use for further computations. As I have read in the manuals/tutorials/mailing-lists I minimized the

RE: [gmx-users] Normal Mode Analysis

Hi, Try renaming it with the extension .trr iso .trj. Berk Date: Tue, 26 May 2009 10:53:32 +0200 From: f.hoffga...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal Mode Analysis Hi, I'm quite a new user of gromacs. I want to do an all-atom normal mode analysis of a small prote

Re: [gmx-users] Normal Mode Analysis

Hi, as I wrote in the first message, I tried renaming it with the extension .trj and yielded segmentation faults. I also tried it with the extension .trr and got the error message: trn version: VERSION 4.0.4 --- Program gmxdump_d, VERSION 4.0.4

RE: [gmx-users] Normal Mode Analysis

Hi, I just saw that 4.0 uses a new mtx format which can also efficiently store sparse matrices. Please try if my modified gmxdump for 4.0.5 works? Store the data below in a file called fix and then do: patch gmxdump.c fix Berk 61a62,63 > #include "s

Re: [gmx-users] Normal Mode Analysis

Hi thanks for your reply. I tried patching as you described it, but I got the error message: patch: `>' expected at line 18 of patch Franzi --- Franziska Hoffgaard PhD Student Bioinformatics & Theo. Biology Group TU Darmstadt 2009/5/26 Berk Hess > Hi, > > I just saw that 4.0 uses a new

RE: [gmx-users] Normal Mode Analysis

Hi, But there is a '>' on line 18, at least in my mail. I tested the patch and it worked for me. Maybe something went wrong when cut and pasting the patch from the email? I can mail you the whole file personally tomorrow, if required. Berk Date: Tue, 26 May 2009 14:47:52 +0200 Subject: Re: [gmx

Re: [gmx-users] constant term in dihedral potential function

Kukol, Andreas wrote: Dear all, I included the following dihedral potential function in a topology: V(phi2) = -5.865 + 7.470 [1+cos(phi2-180°)] + 3.99 [1+cos(2 phi2)] + 1.1 [1+cos(3 phi2-180°)] The problem is about representing the constant term -5.865. Using equation 4.61 (Gromacs 4.0 manua

[gmx-users] solution molecules cannot be set by mdrun after neutralization

Hi everybody, I neutralized my system with the commands: $grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p 4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr $grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb

[gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Thanks, Stefano. Stefano M

Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason?

Re: [gmx-users] Viscosity using periodic perturbation method

Dear Herk: Thank you so much for your help! Maybe the way I asked make it confusing. I read your paper: " Determing the shear viscosity of model liquids from molecular dynamics simulations" You used NVT. My question is which one is better? NPT or NVT? Or you can use either of them. "Strictly sp

[gmx-users] Shared library version binary on CYGWIN

Dear GROMACS users: I'd like to get small sized shared library version GROMACS binary on windows-PC with CYGWIN (to use in some course). Even configured with "--enable-shared", the compiled binary set looks not the shared library version (no DLLs and the total binary set size was over 100MB). Act

Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

Stefano Meliga wrote: Hi again, I've tryed to perform the same preprocessing and EM steps without distance constraints and the situation improves a lot. I get no warnings in the steepest descent EM and only one molecule cannot be set in the conjugate gradient EM. Can you see the reason? Yes

[gmx-users] gmxtest

Dear all, Does your GMX 4 past the gmxtest package in the gmx wiki ? My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and some kernel issues failed. I use standard packages and everything looks find. The simulation result are good and identical to gromacs 3.3.3. But, still

Re: [gmx-users] Shared library version binary on CYGWIN

Makoto Yoneya wrote: Dear GROMACS users: I'd like to get small sized shared library version GROMACS binary on windows-PC with CYGWIN (to use in some course). Even configured with "--enable-shared", the compiled binary set looks not the shared library version (no DLLs and the total binary set si

Re: [gmx-users] gmxtest

Simba Xiao wrote: Dear all, Does your GMX 4 past the gmxtest package in the gmx wiki ? My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and some kernel issues failed. That's normal at the moment, unfortunately. Future releases of gmxtest will probably fix the non-kernel

Re: [gmx-users] gmxtest

Mark Abraham wrote: Simba Xiao wrote: Dear all, Does your GMX 4 past the gmxtest package in the gmx wiki ? My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and some kernel issues failed. That's normal at the moment, unfortunately. Future releases of gmxtest will probab

[gmx-users] Shared library version binary on CYGWIN

Dear Mark and GROMACS users: Mark wrote. > You can't build DLLs since the cygwin build tools are unix-style, and > the GROMACS build strategy is unix-specific. --enable-shared also > probably won't work for unix-style shared libraries, because the dynamic > linker is probably the Windows ld.exe

RE: [gmx-users] Lennard-Jones 9-6 potential problems

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Re: [gmx-users] Lennard-Jones 9-6 potential problems

>> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org <ma

Re: [gmx-users] Lennard-Jones 9-6 potential problems

zhangjianguo2002 wrote: Firstly, thanks Berk and David van der Spoel for your replies. Maybe I have not explain my problems clearly, there is only one type of particle,namely one full-atom benzene molecule is replaced by one coarse-grained benzene particle,so there in no non-bonded inter