[gmx-users] Charges in SW water model

-- ## Andreas Kring, Ph.D.-student University of Copenhagen Niels Bohr Institute Universitetsparken 5 DK-2100 Copenhagen Denmark Phone Office (D304): (+45) 35 32 04 91 Home: (+45) 77 42 55 78 Mobile:(+45) 61 77 55 78 E-mail: [EMAIL

[gmx-users] MD run, polarizable molecules, EM did not converge

Hello all. I've been searching the archives with no luck so here goes: I am using shell molecular dynamics to simulate a hydroxide ion dissolved in water. I have been using the steepest descent minimizer (tried in the range from 30 to 70 steps) to minimize the system, but I'm not

Re: [gmx-users] About the gromacs 4.0 manual and parallel running

2. How to run a parallel simulation with Gromacs 4.0? Are there any special tips for a optimized parallel run? I've tried a set of runnings but found the accelerations are not good enough as I expected. I do something like this (for 8 CPUs): $ grompp -c system.gro -p topology.top -f

Re: [gmx-users] Gromacs-4.0: 4 CPUs crashes, works on 1 CPU

Berk Hess skrev: Hi, Could you file a bugzilla report and attach the tpr file? Please also mention at what step you get this error (run mdrun -v to get the step numbers). Berk Sure, no problem. Regards Andreas ___ gmx-users mailing list

Re: [gmx-users] question about default parameter for g_hbond

Thomas Schlesier skrev: Hi all, does somebody know from where the default parameters for g_hbond (angle Acceptor-Hydrogen-Donor = 30° ; distance Acceptor-Donor = 0.35nm) are? I found nothing in the manual about that. Maybe you can find a hint in Luzar et al., J. Chem. Phys., 98, 8160 (1993)

[gmx-users] Gromacs-4.0: 4 CPUs crashes, works on 1 CPU

Hi all. I have just installed GROMACS 4.0. My system consists of one hydroxide ion and 999 polarizable water molecules. When the system is minimized (using only one CPU) with a steepest descent minimizer, there are no problems. But when I try to minimize exactly the same system using 4 or 8

Re: [gmx-users] Gromacs-4.0: 4 CPUs crashes, works on 1 CPU

Andreas Kring skrev: Hi all. I have just installed GROMACS 4.0. My system consists of one hydroxide ion and 999 polarizable water molecules. When the system is minimized (using only one CPU) with a steepest descent minimizer, there are no problems. But when I try to minimize exactly the same

[gmx-users] Charge groups, PME and ions

Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent). For this molecule it is not possible to make charge

Re: [gmx-users] Charge groups, PME and ions [SOLVED]

David van der Spoel wrote: Andreas Kring wrote: Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent

Re: [gmx-users] Bonds missing in VMD visualization [SOLVED]

, 2008 at 5:59 AM, Andreas Kring [EMAIL PROTECTED] wrote: Thank you for your reply. I tried the following: VMD computes distances between pairs of atoms to draw a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL

Re: [gmx-users] Bonds missing in VMD visualization

Thank you for your reply. I tried the following: VMD computes distances between pairs of atoms to draw a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL should be around 1.76A. In 1,1,1-trichloroethane

[gmx-users] Bonds missing in VMD visualization

Hello, I have run an MD simulation of 1000 1,1,1-trichloroethane molecules and it all worked nicely. But when I try to visualize the trajectory file in VMD some of the C-Cl bonds are missing (although all the atoms appear on the screen - only bonds are missing)? Can I do anything to fix

Re: [gmx-users] Save all MD snapshot

Collins Nganou skrev: Dear Users. Greetings. Please someone can tell me how can I proceed to save all MD snapshot for a long time simulation after equilibration. You can set the parameters below to the value 1 in the configuration file for mdrun. nstxout = 1 nstvout = 1 nstfout = 1

Re: [gmx-users] Arguments to g_rdf [SOLVED]

Exactly what I was looking for! Thanks a lot! /Andreas Justin Lemkul skrev: Is this what you are looking for? http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive -Justin Andreas Kring wrote: Hello all, Is it somehow possible to pass arguments to g_rdf from the command

Re: [gmx-users] grompp error, invalid line in .gro file [SOLVED]

Your formatting is incorrect. The .gro format is a very old GROMOS fixed format (not free format). See the manual for the details: http://www.gromacs.org/documentation/reference/online/gro.html Thanks a lot. Now everything works perfectly! /Andreas

[gmx-users] grompp error, invalid line in .gro file

Hello all. I'm trying to simulate an argon liquid. The OPLS-AA force field is used with the files from /usr/local/gromacs/share/gromacs/top. But I get an error when I run $ grompp -f NVT.mdp -c Ar.gro -p Ar.top --- Program grompp, VERSION

Re: [gmx-users] grompp error, invalid line in .gro file

Justin A. Lemkul skrev: Just thinking out loud, but maybe Argon is too long of a name for the residues. The longest I think I've seen is 4 characters (something like LYSH or ARGN, for example). Maybe the length of the name is throwing off the formatting. Why don't you try again with a residue

[gmx-users] Re: Wrong heat capacity (water)

Continuation of thread http://www.gromacs.org/index.php?option=com_wrapperItemid=84 (answered by David van der Spoel) Hello all, I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules, density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This works out

[gmx-users] Wrong heat capacity (water)

Hello all, I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules, density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This works out fine, i.e. I get a correct radial distribution function (g_OO), but the heat capacity (C_V) is wrong. I calculated it using the

[gmx-users] atomtypes, parameters in file do not match parameters in manual

Hello all. I'm new to Gromacs, so sorry for this (probably naive) question: In Table 5.3 in the Gromacs manual version 3.3, the parameters for [atomtypes] are: atom type, mass, charge, particle type, V and W. In the Gromacs directory containing the the force fields