[gmx-users] mdrun -nice integer

Hi for the mdrun command, what does "-nice integer" mean? I have read the manual, but still have no idea for this. Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] box size

Hi 1. in the last row of .gro file, the three number represent the length of the box on X, Y , and Z directions in nanometer. Right?? 2. for the editconf command, editconf -d Distance_between_the_solute_and_the_box bt cubic Right?? what are the differences between the three number in th

[gmx-users] simulate Gas Phase system

Hi to simulate the gas phase system, before running MD on the gas phase system I have to use the "editconf" command. But, I DO NOT use "genbox" command. Right?? thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mail

FW: [gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs

From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: RE: [gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs Date: Fri, 4 Jul 2008 10:14:14 +0200 Hi, It is completely clear to me if your 1-4 and 1-5 interactions use the same potential

[gmx-users] Re: QMMM memory problem

Was gromacs configured with the --with-qmmm-gaussian option? Is gaussian installed and running as well? can you make a tar file of the input files (topology, index, mdp, configuration) and send it directly to me (i.e not via userlist)? Gerrit -- Message: 2 Dat

Re: [gmx-users] simulate Gas Phase system

Chih-Ying Lin wrote: Hi to simulate the gas phase system, before running MD on the gas phase system I have to use the "editconf" command. But, I DO NOT use "genbox" command. I'm new to Gromacs, but I think that if you do that you will running simulation in vacuo. Maybe it a good approximat

Re: [gmx-users] mdrun -nice integer

Hi "integer" means number, but not decimal. You can choose 2 or 3, but you can not choose 2.5 or 2.2 The nicevalue value is one way of measure the priority of your process. You can choose any value between -20 and 19. A processe with nice value = -20 it's very high priority and with nice val

Re: [gmx-users] box size

Chih-Ying Lin wrote: Hi 1. in the last row of .gro file, the three number represent the length of the box on X, Y , and Z directions in nanometer. Right?? These values represents the real dimensions of the box 2. for the editconf command, editconf -d Distance_between_the_solute_and_the

[gmx-users] drawing chemicals 2d sketchs

Hi List, OK, it may be a bit off-topic, but I am looking for a software to, given a pdb of a small molecule, draw a 2d chemical structure, but: - if possible free - if possible for Mac Osx, then Linux (perhaps Windows) - able to show labels numbers and atom type. If someone knows a program with

Re: [gmx-users] drawing chemicals 2d sketchs

Hi, On Friday, 4. July 2008 12:15, Alan wrote: > Hi List, > > OK, it may be a bit off-topic, but I am looking for a software to, > given a pdb of a small molecule, draw a 2d chemical structure, but: > > - if possible free > - if possible for Mac Osx, then Linux (perhaps Windows) > - able to show l

Re: [gmx-users] segmentation fault during MD

huan wrote: Dear gmx users and developers. I was running a simulation with 5 ns. But it stated "segmentation fault" at time around 1 ns, and the simulation was stopped. By the way, i faced 2 warning during running the Grompp, it stated there:" warning 1 No default Ryckaert-Bell type

Re: [gmx-users] simulate Gas Phase system

Nuno Azoia wrote: Chih-Ying Lin wrote: Hi to simulate the gas phase system, before running MD on the gas phase system I have to use the "editconf" command. But, I DO NOT use "genbox" command. I'm new to Gromacs, but I think that if you do that you will running simulation in vacuo. May

Re: [gmx-users] box size

Chih-Ying Lin wrote: Hi 1. in the last row of .gro file, the three number represent the length of the box on X, Y , and Z directions in nanometer. Right?? These values represents the real dimensions of the box 2. for the editconf command, editconf -d Distance_between_the_solute_and_the

[gmx-users] topology using prodrg

Dear users, I am modeling polymer surface. I need topology for polystyrene. I used prodrg earlier version and beta version but in both cases I get topology for only GROMOS87 force field. Can not I get topology for force filed GROMOS96 ? also can anybody let me know what is .itp file for GOMOS87 f

Re: [gmx-users] box size

Hi, Read a bit more carefully though. A cubic box is based on the circumscribed sphere of the solute, dilated with the desired distance between the solute and the wall (and it has nothing to do with calculation of the solvation surface, which to me sounds to be related to solvent accessible surfac

Re: [gmx-users] topology using prodrg

Are you sure you used prodrg beta? http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta 2008/7/4, h a <[EMAIL PROTECTED]>: > > Dear users, > > I am modeling polymer surface. I need topology for polystyrene. I used > prodrg earlier version and beta version but in both cases I get topology > for

[gmx-users] segmentation fault during MD and develop parameter

Dear all Gmx users n developers, I am a beginner of Gromacs user, hence I am quite new to the system..May i know how to develop the missing dihedral parameter? Any guide n comments will be appreciated. Thanks --- On Fri, 7/4/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. L

[gmx-users] Re: segmentation fault during MD and develop parameter

huan wrote: Dear all Gmx users n developers, I am a beginner of Gromacs user, hence I am quite new to the system..May i know how to develop the missing dihedral parameter? Any guide n comments will be appreciated. Thanks No one here is going to be able to help, aside from the stand

[gmx-users] Atom CD in residue ILE 1 not found in rtp entry with 19 atoms

Hello list, I tried out the Membrane Builder at www.charmm-gui.org, which generates CHARMM input files for a combinded membrane-protein system and it looks quite good. The conversion CHARMM -> GROMACS is a bit tricky, I know, but I wanted to try it, though: Using the Perl script on http://www.gro

[gmx-users] rot-diffusion

Dear users, Is it possible to evaluate the rotational diffusion of proteins using gromacs tools ?? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

[gmx-users] Restraining molecular symmetry

Dear All, I have two queris First: I am simulating a tetramic protein, each monomer with 150 amino acids, in gromacs 3.3.1. The protein molecule has a proper 4 fold symmetry. But during simulation the symmetry is some what not retained. Two monomers which should be related by ~180 degree rotation

Re: [gmx-users] Atom CD in residue ILE 1 not found in rtp entry with 19 atoms

There are a few nomenclature issues with the ffcharmm files. Rename CD1 to CD and things should work fine, as far as ILE is concerned. I recalled the .tdb files needing some work as well to meet the format requirements. -Justin Volker Wirth wrote: Hello list, I tried out the Membrane Buil

[gmx-users] segmentation fault during MD and develop parameter

Dear all Gmx users n developers, I am happy and appreciate with all the help n suggestions you all have given to me. Here is my molecule look likes.: C-C-C-C-C-C-C-C-C=C-C-C-C-C-C-C-C-C | O