[gmx-users] Re: gmx-users Digest, Vol 60, Issue 89

nd covariance analysis, it is giving Segmentation Fault. Am I doing anything wrong. Any suggestion is welcome. Regards, Anirban Ghosh Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Add more friends to your messenger and enjoy! Go t

Re: [gmx-users] Implicit Solvent System - Energy Minimization

Grace Tang wrote: Sorry, I wasn't too clear in the first message. I will be using OpenMM Gromacs, which does support implicit solvent. My current energy minimization steps only lower the energy to -5E3. Is this okay considering water is not around? Probably. Is is necessary to do equilibr

[gmx-users] improper dihedrals for OPLS

Dear gmx-users, I am confused about the exact formula for improper OPLS dihedrals in gromacs. Is it periodic, e.g. V[1-cos(2x)], or harmonic, e.g. [V*(x-x0)^2]? In ffoplsaa.rtp, it says in the Col 4 in the following the type of improper dihedrals to be 1, which I believe is a harmonic function. T

Re: [gmx-users] Implicit Solvent System - Energy Minimization

Sorry, I wasn't too clear in the first message. I will be using OpenMM Gromacs, which does support implicit solvent. My current energy minimization steps only lower the energy to -5E3. Is this okay considering water is not around? Is is necessary to do equilibration if I am using implicit solven

Re: [gmx-users] Problem with grompp?

Hoof, B. van wrote: Hi everyone, Since I am a new user of Gromacs, this problem is probably rather trivial, but I hope one of you would like to help me nonetheless. I have created a starting structure in a not very optimal situation, which I have then minimized. To continue, I would like to

[gmx-users] Problem with grompp?

Hi everyone, Since I am a new user of Gromacs, this problem is probably rather trivial, but I hope one of you would like to help me nonetheless. I have created a starting structure in a not very optimal situation, which I have then minimized. To continue, I would like to equilibrate the system

Re: [gmx-users] Topologies and charges for large organic ligands

Hi, The answer is (or should be) in: @article{Oostenbrink2004, Author = {Oostenbrink, C. and Villa, A. and Mark, A. E. and Van Gunsteren, W. F.}, Title = {A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6},

[gmx-users] Topologies and charges for large organic ligands

Dear colleagues, In 53a6, the topology and charges for (NAD+) nicotinamide adenine dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form (without aromatic hydrogens). Is there anyone who can tell me how such a molecule was charge group parameterized? (with sufficient certaint

Re: [gmx-users] g_covar Segmentation fault

Anirban Ghosh a écrit : Hi ALL, I have a system of beads with which I ran a CGMD (coarse grained MD) using NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I converted the trajectory in .trr format Convert a dcd file into a trr file is not that straightforward. How did y

Re: [gmx-users] g_covar Segmentation fault

Anirban Ghosh wrote: Hi ALL, I have a system of beads with which I ran a CGMD (coarse grained MD) using NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I converted the trajectory in .trr format and made an index file of the entire system (45 beads). But now when I try t

[gmx-users] g_covar Segmentation fault

Hi ALL, I have a system of beads with which I ran a CGMD (coarse grained MD) using NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I converted the trajectory in .trr format and made an index file of the entire system (45 beads). But now when I try to run g_covar using the

Re: [gmx-users] Implicit Solvent System - Energy Minimization

Grace Tang wrote: Hello All, I am doing energy minimization on a protein crystal structure to relax it. Afterwards, I plan to run md simulation with implicit solvent. I am new at this and have many questions. 1. Should the implicit solvent conditions be enabled when I run the energy minimiz

Re: [gmx-users] the position_restraints

You may have defined position restraints that exceed the number of atoms present your system, or define them in a wrong manner. Check manual and previous posts. On Apr 15, 2009, at 12:29 AM, Justin A. Lemkul wrote: He, Yang wrote: HI Justin, I just use the mdrun command and then get such e

Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault

Hi, I received a similar error during an equilibration by steepest descent in which I had posed constraints on water, leaving the protein free to move. I suggest to control your mdp file... maybe you did the same thing and the system collapsed or exploded (you can see that reading the log file: if

Re: [gmx-users] problem during inflatgro process

Hi Nitu, First of all, please try to use proper english for communication. This way 'u don't make it EC-r 4 us'. Second, you'd be better off getting some understanding of how topologies and coordinate files are put together before trying to do these things. A question like 'can I remove something

[gmx-users] Implicit Solvent System - Energy Minimization

Hello All, I am doing energy minimization on a protein crystal structure to relax it. Afterwards, I plan to run md simulation with implicit solvent. I am new at this and have many questions. 1. Should the implicit solvent conditions be enabled when I run the energy minimization? 2. What minimum

Re: [gmx-users] How to restrain ligand atom position

Hi Hitesh, The posre.itp file only contains a header [ position_restraints ] followed by a list of atom numbers and restraint force constants. Check chapter 5 of the manual for how and what. For a ligand it's probably best to directly add the [ position_restraints ] section in the file with the [

[gmx-users] How to restrain ligand atom position

Dear all, I have generated .itp file for ligand using PRODRG server which i included in topology file. Now for position restrained dynamics, i wanted to restrain atom positions for ligand and protein . But porse.itp which generated using pdb2gmx contain restraints for protein only. Kindly provide