Re: [gmx-users] GMX-Installation2

nanogr...@ymail.com wrote: Dear Jussi, Hi, Thanks for your help, Because of some problems with fedora 10, I installed Fedora 11. Unfortunately, I can not understand the instructions of your e-mail. I am new with Gromacs! That won't get you any more help. We're all busy people, and we'r

Re: [gmx-users] problem during simulation of dna-protein complex

Hi Nitu, Energy minimization is only to remove some strain from your system. You probably don't want to include position restraints there. After energy minimization you typically run a short MD run in which you use position restraints such that the protein/DNA doesn't move to much, but the water c

[gmx-users] GMX-Installation2

Dear Jussi,   Hi,   Thanks for your help,   Because of some problems with fedora 10, I installed Fedora 11.   Unfortunately, I can not understand the instructions of your e-mail. I am new with Gromacs!   Now, all of required files of gromacs 4 are completely installed on computer, however, it ca

Re: [gmx-users] How to set fourierspacing?

wuxiao wrote: > Dear colleagues, > I use PME to consider coulomb interactions. It seems that the > fourierspacing is an important parameter. When it is set a larger value, > the calculation can be much faster. But what is the disadvantages of > using a larger value? I wish to get you help. Fa

[gmx-users] How to set fourierspacing?

Dear colleagues, I use PME to consider coulomb interactions. It seems that the fourierspacing is an important parameter. When it is set a larger value, the calculation can be much faster. But what is the disadvantages of using a larger value? I wish to get you help. Best Regards, Chaofu

Re: [gmx-users] disable ulimit

Thanks Ansgar   We'll try it.   Dr Gustavo Fioravanti Vieira  Núcleo de Bioinformática do Laboratório de Imunogenética   Bolsista PNPD do Programa de Pós-Graduação em Genética e Biologia Molecular UFRGS --- Em seg, 29/6/09, Ansgar Esztermann escreveu: De: Ansgar Esztermann Assunto: Re:

Re: [gmx-users] umbrella sampling: pdo file not generated

Gustavo Velardez wrote: Hi all, I ran a calculation using GROMACS 4.0.3 and this command line: mpirun -np 8 mdrun_mpi -v -s $mol.tpr -pi $inp.ppa -pd $inp.pdo -po pullout.ppa -pn index5000.ndx -g $mol.log > & $mol.out I think everything is OK (it's working on GROMACS 3.3), but the pdo file h

Re: [gmx-users] umbrella sampling: pdo file not generated

Justin A. Lemkul skrev: Gustavo Velardez wrote: Hi all, I ran a calculation using GROMACS 4.0.3 and this command line: mpirun -np 8 mdrun_mpi -v -s $mol.tpr -pi $inp.ppa -pd $inp.pdo -po pullout.ppa -pn index5000.ndx -g $mol.log > & $mol.out I think everything is OK (it's working on GROMACS

[gmx-users] umbrella sampling: pdo file not generated

Hi all, I ran a calculation using GROMACS 4.0.3 and this command line: mpirun -np 8 mdrun_mpi -v -s $mol.tpr -pi $inp.ppa -pd $inp.pdo -po pullout.ppa -pn index5000.ndx -g $mol.log > & $mol.out I think everything is OK (it's working on GROMACS 3.3), but the pdo file has NOT been generated.

[gmx-users] Rigid body-LINCS warning

Dear Gromacs users,I try to run a molecular dynamics simulation of a polyoxometalate. I want the molecule to behave as a rigid body except for one peptidic chain bound to it. To achieve this, I constrain all the relative distances between every possible couple of atoms in the structure. I add th

Re: [gmx-users] norm of force = nan error

P.R.Anand Narayanan wrote: dear justin, i recently got this error: Norm of force =nan (not a number) while doing a 5000 step energy minimization. the em gets over in just 1 step and this error is shown.how do i rectify this? You either have severe atomic overlap or an othe

Re: [gmx-users] make index group

Mark Abraham wrote: Bing Bing wrote: Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx > 15 & a Cxx |... >q i've got this error :- Group 15 not exist. So use a group that does exist. If you're copying an index group creation reci

[gmx-users] problem during simulation of dna-protein complex

Dear Tsjerk Thanks for your right suggestion. It works successfully for dna-protein complex simulation. i want to ask one more thing , can I use parameter file for energy minimisation which i have used for membrane protein simulation or can u suggest me what changes I have to ma

Re: [gmx-users] make index group

Bing Bing wrote: Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx > 15 & a Cxx |... >q i've got this error :- Group 15 not exist. So use a group that does exist. If you're copying an index group creation recipe from some tutorial,

Re: [gmx-users] GMX Installation

On Wed, 2009-07-01 at 01:01 -0700, mahmoud wrote: > Dear GMX Users, > > I want to Install Gromacs on Fedora 10 x86_64. I downloaded the rpm > files of FFTW and Gromacs, however, I can not install the gromacs yet. > > Please guide me if you have information on this case. You can just install th

[gmx-users] norm of force = nan error

dear justin, i recently got this error: Norm of force =    nan (not a number) while doing a 5000 step energy minimization. the em gets over in just 1 step and this error is shown.how do i rectify this? thank you. Love Cricket? Check out live scores, photos, video highlights

Re: [gmx-users] Re: Problem with AMBER-GROMACS DNA database residue

Hi, Alan Thank you very much for your quick answer. You understand well my problem... I normally use amb2gmx for proteins, and, changing some residue names (ex. CYM-->CYS..), it works correctly... It's the first time that I work with DNA, and I have this problem... thank you for your help Rubben 2

[gmx-users] make index group

Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx > 15 & a Cxx |... >q i've got this error :- Group 15 not exist. I did not make index before I proceed with grompp for the mdrun, is it cause by this? thanks. Regards, bing _

[gmx-users] Re: Problem with AMBER-GROMACS DNA database residue

Hi there, Not really clear what you did or want to do, so I'll do assumptions. If your have you prmtop and inpcrd files working fine with AMBER (sand or pmemd) then you just want to run this with GMX (mdrun ...). So, you can try amb2gmx.pl program or (better), look at acpypi.googlecode.com, and

[gmx-users] Problem with AMBER-GROMACS DNA database residue

Hi, gmx-users, I have a problem to "translate" nitrogen base residue names from AMBER to GROMACS. I have simulated with AMBER a DNA-protein complex, then i have changed in the prmtop file the standard nitrogen bases as DT--> DTHY, DG-->DGUA, DC-->DCYT, DA-->DADE, in order to "translate" the MDs fr

[gmx-users] Energy analysis by mdrun -rerun

hi,gmx-users I run a simulation with mdrun -rerun like this: mdrun -s rerun.tpr -rerun md.trr -o rerun.trr -e rerun.edr -g rerun.log Then I run g_energy -f rerun.edr -o LJ-SR.xvg I observed a strange behavior that the avarge value of LJ-SR in the screen is very different from the value in

Re: [gmx-users] How to avoid generating wrong dihedrals?(Tsjerk)

wuxiao wrote: > Dear Tsjerk and other gmx users and developers, > I use OPLS-AA force field to model a dendrimer PAMAM. And the addition > of hydrogens is found correct. The rtp files were written for the core, > middle and end repeating units, respectively. The both repeating units > cause t

Re: [gmx-users] How to avoid generating wrong dihedrals?(Tsjerk)

Dear Tsjerk and other gmx users and developers, I use OPLS-AA force field to model a dendrimer PAMAM. And the addition of hydrogens is found correct. The rtp files were written for the core, middle and end repeating units, respectively. The both repeating units cause the problem. When I del

Re: [gmx-users] Installation problem:fftw3f lib. not found.

* Shobhit Kudesia [2009-06-30 21:19:47 -0400]: Hi, I installed fftw as follows (creating single- and double-precision versions) : ./configure --enable-threads --enable-float --prefix=/home/kudesias/fftw make make install make distclean ./configure --enable-threads --prefix=/home/kudesias/f

Re: [gmx-users] Table Functions

Devin Averett wrote: Hi- I am trying to add an extra repulsive potential for neighboring hydroxyl groups on a carbon chain and have heard that this can be done using table functions. Is there a good resource on how to create these table function files or even someplace where I could get an

Re: [gmx-users] GMX Installation

> Dear GMX Users, >   > I want to Install Gromacs on Fedora 10 x86_64. I downloaded the rpm files > of FFTW and Gromacs, however, I can not install the gromacs yet. >   If you want some help from the mailing list, you have to be a bit more specific about your problem. You can also read the documen

Re: [gmx-users] GMX Installation

mahmoud wrote: Dear GMX Users, I want to Install Gromacs on Fedora 10 x86_64. I downloaded the rpm files of FFTW and Gromacs, however, I can not install the gromacs yet. Please guide me if you have information on this case. You should search the web for information on installing RPMs, or f

[gmx-users] GMX Installation

Dear GMX Users,   I want to Install Gromacs on Fedora 10 x86_64. I downloaded the rpm files of FFTW and Gromacs, however, I can not install the gromacs yet.   Please guide me if you have information on this case.     Thanks.   Mahmoud< ___ gmx-us