[gmx-users] missing atoms

Dear gmx users   I have a protein molecule with few missing residues, a Lys with CG, CD, CE, NZ missing atoms, and a Val with CG1, CG2 missing atoms. I noticed that pdb2gmx reads the pdb file and places the missing atoms. First I want to know whether gromacs places only missing atoms or it pl

[gmx-users] parallel in duals?

Ok, I know this subject have been discussed in the past. But I started to wander if the basic conclusion (do not use in parallel, you should rather use on job for each core) is still up, and if it is, if there is any hope of change in a foresight future, as well on how much real loss is observed f

Re: [gmx-users] Deshuffling atoms vs. residues

Okay, now I have a partial answer to my own question. Apparently, when using the -sort and -shuffle options, the indexfile written by grompp undoes the shuffling, but not the sorting, so to speak. This became clear when I noticed that using just -shuffle without -sort produced the very same inde

[gmx-users] g_sdf

Dear Gromacs-users, I would like to use the analysis tool g_sdf, but couldn't find in the download section. If someone has the file, would you like to send me that ? Does it work with gromacs-3.3.1? Thank you very much for your help in advance. best, Hwankyu. _

[gmx-users] Deshuffling atoms vs. residues

Hi, I suspect this might be a stupid question, but we've all been beginners one day, haven't we? I have generated a shuffled/sorted trajectory (grompp -sort -shuffle) of a lipid bilayer, which I have then deshuffled using trajconv and the index file. In the resulting file, each residue is in o

Re: [gmx-users] Disulphide bonds

Cesar Araujo wrote: Hi, Anybody knows if there is some way to tell pdb2gmx to recognize automatically S-S bonds and not through the modification of specbond.dat file and -ss option??? it does if they are within the normal distance. are your pdb files ok? Regards, César.- -

Re: [gmx-users] a standalone xtcio library

LI Daobing wrote: hello, I prepared an standalone xtcio library[1] from gromacs 3.3.1. I prepared this because I have had some bad experience in directly using the xtc part from gromacs[2]. now it provide a single and a double precision library, and it can work. There are many things need to do,

[gmx-users] g_rdf and structure factor

Dear gromacs users, I am using Gromacs 3.3 to simulate a coarse-grained molecule which contains atom B and L. The atom B and L are defined myself. When the simulation finished, I tried to use g_rdf to calculate the static structure factor. But it gave the error message: - Pro

RE: [gmx-users] Segmentation fault in Gromacs parallel run

Hi, The error has been resolved. This problem occurred in Gromacs 3.2.1. Using Gromacs 3.3.1 instead, it doesn't happen any more. George From: "Ge Sunny" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Segmentation fault in Grom

[gmx-users] problem using pairtypes 2, 3 for free-energy decoupling

Dear Michael, Berk, all I'm currently trying to use GROMACS for calculation of solvation free energies for small molecules in water and hexane. Searching through the mailing archives I found the following method to decouple solvent-solute interactions: Berk Hess Wed Mar 1 09:30:25 CET 2006 wrote

[gmx-users] Segmentation fault in Gromacs parallel run

Hi, I have a problem in running Gromacs in parallel. My simulation can be successfully run on 1 cpu. However, when running in parallel on more than one cpu (e.g., 4 cpus), there always occurs a Segmentation fault error: ERROR: 0031-250 task 1: Segmentation fault I'm running parallel Gromacs

Re: [gmx-users] langevin dynamics

Gerrit is right, with "sd", the friction is set by tau_t, as described in the section on SD in the manual. In my hands, different tau_t with sd does make a significant difference in what goes on... David On 7/31/06, Gerrit Groenhof (RUG) <[EMAIL PROTECTED]> wrote: I think you do not use the bd

[gmx-users] Re: It consults in Gromacs (Carolina, Venezuela)

Carolina Silva wrote: Many greetings Please excuse my level for English. I am learning it I am also trying to learn to handle the program GROMACS I want to simulate a pure ethylbenzene mixture (first step ) but I hoped to obtain it from phenylalanine, so that I saw that the blocks of construcion

Re: [gmx-users] langevin dynamics

I think you do not use the bd_fric in combination with sd, but with bd, the friction is set by the tau_t instead. Did you als use different parameters for that? For bd, you would use the friction bd_fric to set the ld friction, but not for sd, but I could be wrong here... Gerrit syma wrote:

[gmx-users] langevin dynamics

Hi, I have been having a few problems running Langevin dynamics and was wondering if anyone can help. I have run both atomistic and coarse grain LD simulations in gromacs 3.1 3.2 and 3.3. The puzzling thing is that changing the value of the frictional constant makes no difference to the simulatio

Re: [gmx-users] Disulphide bonds

I use the option -merge with my SS-linked peptides, and pdb2gmx always asks me if I want to join my cysteines with a bond. If they're internal to the protein, perhaps it's either that they're too far apart, or you need -ignh as otherwise they've got hydrogens on and potentially can't bond. --- Ce

[gmx-users] Disulphide bonds

Hi,   Anybody knows if there is some way to tell pdb2gmx to recognize automatically S-S bonds and not through the modification of specbond.dat file and -ss option???   Regards, César.-   ---Cesar Araujo, Lic. of ChemistryDepartment of Mo

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi Art, you run a small system (4800 atoms) on a lot of CPUs (64). In the md.log file it says that you have 2 grid points per CPU for the parallel FFT (local_nx). There is indeed one limitation to the PME code in 3.3.1: you need at least 0.5*pme_order grid points per CPU. Your pme_order is 6. So