Re: [gmx-users] atomname -> atomic number

Mark Abraham wrote: > Daniel Baum wrote: >> Hi, >> >> I would like to write a reader for *.gro files, but I couldn't find any >> information about how to map the atomname to the atomic number. Can >> anyone shed some light on this problem? I would be most grateful. > > It's an ill-defined problem..

Re: [gmx-users] atomname -> atomic number

Hi, I would like to write a reader for *.gro files, but I couldn't find any information about how to map the atomname to the atomic number. Can anyone shed some light on this problem? I would be most grateful. The ff*nb.itp file contains already the atomic numbers of the atoms. Probably n

Re: [gmx-users] Making PDB file

Hi, On Thursday, 15. May 2008 08:20, User Gromacs wrote: > Dear Users of Gromacs, > > This is Alex. I am a new user of Gromacs. As you know to do my simulation > with Gromacs, I need to have a PDB file. Let me know a powerful software to > construct my PDB file in Mac OS X? I know the Materials St

Re: [gmx-users] atomname -> atomic number

Mark Abraham wrote: Daniel Baum wrote: Hi, I would like to write a reader for *.gro files, but I couldn't find any information about how to map the atomname to the atomic number. Can anyone shed some light on this problem? I would be most grateful. It's an ill-defined problem... is "HG" mercu

Re: [gmx-users] Making PDB file

User Gromacs wrote: Dear Users of Gromacs, This is Alex. I am a new user of Gromacs. As you know to do my simulation with Gromacs, I need to have a PDB file. Let me know a powerful software to construct my PDB file in Mac OS X? I know the Materials Studio is a very good software. But unfortun

[gmx-users] Making PDB file

Dear Users of Gromacs,This is Alex. I am a new user of Gromacs. As you know to do my simulation with Gromacs, I need to have a PDB file. Let me know a powerful software to construct my PDB file in Mac OS X? I know the Materials Studio is a very good software. But unfortunately it does not work in M

Re: [gmx-users] atomname -> atomic number

Daniel Baum wrote: Hi, I would like to write a reader for *.gro files, but I couldn't find any information about how to map the atomname to the atomic number. Can anyone shed some light on this problem? I would be most grateful. It's an ill-defined problem... is "HG" mercury or some kind of hy

Re: [gmx-users] Range checking error

[EMAIL PROTECTED] wrote: My initial input file is a model which was generated using Modeller, and it is a part of the original structure. I am considering fragments of a particular structure for my analysis. Could this be a possible problem for running a simulation?? I suppose there is a problem

Re: [gmx-users] Range checking error

My initial input file is a model which was generated using Modeller, and it is a part of the original structure. I am considering fragments of a particular structure for my analysis. Could this be a possible problem for running a simulation?? I suppose there is a problem when I try to convert this

[gmx-users] atomname -> atomic number

Hi, I would like to write a reader for *.gro files, but I couldn't find any information about how to map the atomname to the atomic number. Can anyone shed some light on this problem? I would be most grateful. Cheers, Daniel ___ gmx-users mailing list

Re: [gmx-users] Range checking error

[EMAIL PROTECTED] wrote: Dear members I happened to get an error which is as follows : Range checking error: I think it is a problem with energy minimisation and neutralising the system. However I tried many ways to solve the issue, it still seems to give me the same error. Could anyone su

[gmx-users] Range checking error

Dear members I happened to get an error which is as follows : Error on node 17, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 17 out of 32 gcq#106: "Step Aside, Butch" (Pulp Fiction) node26:19.MPID_CH_Abort: node26:19.Aborting program! node26:17.MPID_CH_Abort: node26

Re: Re: [gmx-users] how to build the input files of an infinite system

Thanks, Mark I am so sorry about my failure to describe my problem clearly. My problem is that while I was doing EM with that infinite system, the Fmax was unreasonably large (~1e4). But just now, I changed the pbc=xyz to pbc=full in my em.mdp file, then it is OK now. So I have a new question

Re: [gmx-users] how to build the input files of an infinite system

silvester.thu wrote: > Hello everyone, > > I am working on a simulation of an infinite system but I do not know how > to build its periodic boundary conditions in GROMACS. My system is a > graphene that is infinite on a certain direction. Surely I can not > generate an infinitely large graphen

[gmx-users] how to build the input files of an infinite system

Hello everyone, I am working on a simulation of an infinite system but I do not know how to build its periodic boundary conditions in GROMACS. My system is a graphene that is infinite on a certain direction. Surely I can not generate an infinitely large graphene for input. So I want to make a f

Re: [gmx-users] distance restrained energy minimisation

jayant james wrote: Hi! I am attempting DISRES energy minimization. I'd like to turn ur attention to the 2nd & 5th line below. these contain a common atom 2711 and the distance in the PDB file to its counterpart (2444 or 2575) is 55 angstroms well within the specified range. See manual sect

[gmx-users] distance restrained energy minimisation

Hi! I am attempting DISRES energy minimization. I'd like to turn ur attention to the 2nd & 5th line below. these contain a common atom 2711 and the distance in the PDB file to its counterpart (2444 or 2575) is 55 angstroms well within the specified range. But still I get a system explode warning!!!

[gmx-users] Pressure and All-bonds

Hi All. I try to use different potential models with an Oh symmetry molecule. I created a topol with nonbond_params, bonds and angles sections, no include etc. Initial configuration comes from another program that deals only rigid bodies, potential parameters come from literature, tested with o

[gmx-users] Semi-isotropic pressure coupling

Hi, I was performing NPT simulation of a water - solid interface and used Berendsen Semi-Isotropic coupling. The solid is a SAM - 11 atoms long and packed together closely to form a surface in the x-y plane. Pcoupl = Berendsen Pcoupltype = semiisotropic;

[gmx-users] Re: gmx-users Digest, Vol 49, Issue 53 bilayer area problem

1. You really must figure out your email issue. Go to http://www.gromacs.org/pipermail/gmx-users/2008-May/034065.html to see what some of us have to wade through to assist you. 2. Avoid changing your subject line when continuing a discussion 3. Did you address Marks comment about " define =

Re: [gmx-users] problem with energy minimization

[EMAIL PROTECTED] wrote: dear gromacs user i am doing simulation of Gal1p protein with ligand and without ligand.i made the system without ligand by removing the ligand from pdb file then i use pdb2gmx for generating topology file and editconf for adding box dimention and add spc water molecules.

Re: [gmx-users] Ramachandran plots in GRACE

Quoting Petr Sklenovsky <[EMAIL PROTECTED]>: > Hello, > > I obtained output from the g_rama binary that calculates Ramachandran plots > of peptide. I tried to plot the rama.xvg data in XMGRACE but my attempt was > unsuccessful. Could you help me? What should I write in the command line? "Unsucces

[gmx-users] Ramachandran plots in GRACE

Hello, I obtained output from the g_rama binary that calculates Ramachandran plots of peptide. I tried to plot the rama.xvg data in XMGRACE but my attempt was unsuccessful. Could you help me? What should I write in the command line? The g_helix binary does not calculate number of helical residu

[gmx-users] problem with energy minimization

dear gromacs user i am doing simulation of Gal1p protein with ligand and without ligand.i made the system without ligand by removing the ligand from pdb file then i use pdb2gmx for generating topology file and editconf for adding box dimention and add spc water molecules.i have not face any problem

[gmx-users] Re: gmx-users Digest, Vol 49, Issue 53 bilayer area problem

yes, the bilayer is from tielman's website. The expected area per lipid at 300K is 57nm2 to 60 nm2 where i have getting only 50 nm2. the rvdw i have used as per the rules i have read from the archive where it was said that 1.8nm to 2.0 nm should be the rvdw. Is there any problem with the compress

Re: [gmx-users] bilayer DMPC

Search the list archive for rvdw with lipids, membranes or similar keywords. Also look the rvdw values used in published work. There have been discussions about balancing attractive and repulsive forces and the cutoff values can have a strong influence on area. And as others pointed, compare

RE: [gmx-users] Energy minimisation problem

You should also do some MD and then look at your molecule and trajectory (bond lengths, angles, etc.), if it becomes distorted. If that is the case, there might be something wrong with your topology. If everything is fine, you should use the energy minimised molecule to build the box, EM again