[gmx-users] Segfault using Verlet-list with Gromacs 4.6.5 - MPI only

Dear gmx developers, I am trying to use Verlet list for MD simulations using MPI parallelization only with Gromacs 4.6.5. However, I am getting a segfault during the initialization of my system before any time step is executed. The simulation runs perfectly when I am either using Group list or

Re: [gmx-users] g_chi-like analysis for nucleic acid residues

Sorry you are looking for dihedrals I have just sow that, I think gmx gangle can not do that. 2014-04-14 23:34 GMT+02:00 Josip Lovrić : > If I understood you correctly, I think you are looking for gmx gangle. It > is part of 5.0 version. You need to install new version. > Check hear > http://www

Re: [gmx-users] g_chi-like analysis for nucleic acid residues

Hi Justin, I tunnel-visioned and completely forgot about the mk_angndx tool. I had written a similar task for use with ptraj. I should have mentioned that I am working with .dcd's produced from NAMD with AMBER ff12SB forcefield and parameters, but that's just a matter of getting pdb2gmx to play

Re: [gmx-users] g_chi-like analysis for nucleic acid residues

If I understood you correctly, I think you are looking for gmx gangle. It is part of 5.0 version. You need to install new version. Check hear http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 2014-04-14 23:09 GMT+02:00 sbowerma : > Hi Justin, > > Thanks for your response. I did

Re: [gmx-users] g_chi-like analysis for nucleic acid residues

On 4/14/14, 5:09 PM, sbowerma wrote: Hi Justin, Thanks for your response. I did see the g_angle tool, but doesn't it have a similar limitation as AMBER's ptraj? From what I can see, I would still need to script out an index file for every single dihedral atom set of interest (which is all of

Re: [gmx-users] g_chi-like analysis for nucleic acid residues

Hi Justin, Thanks for your response. I did see the g_angle tool, but doesn't it have a similar limitation as AMBER's ptraj? From what I can see, I would still need to script out an index file for every single dihedral atom set of interest (which is all of them and I have over 1k residues). Whil

Re: [gmx-users] adding ATP parms to AMBER99

Yes indeed - and thanks to Alexey and Tom for the .rtp/hdb and .itp files, respectively! Much appreciated. On Apr 12, 2014, at 1:18 AM, Alexey Shvetsov wrote: > В письме от 11 апреля 2014 14:11:09 пользователь Justin Lemkul написал: >> On 4/11/14, 1:43 PM, Stephen N. Floor wrote: >>> Hi groma

Re: [gmx-users] g_chi-like analysis for nucleic acid residues

On 4/14/14, 4:33 PM, sbowerma wrote: Hello all, I am currently looking at the g_chi analysis tool. I would like to create a time distribution of dihedral angle values for a dna-protein system, with the end-goal of using this distribution in a mutual information calculation. Unfortunately, I s

[gmx-users] g_chi-like analysis for nucleic acid residues

Hello all, I am currently looking at the g_chi analysis tool. I would like to create a time distribution of dihedral angle values for a dna-protein system, with the end-goal of using this distribution in a mutual information calculation. Unfortunately, I see that the g_chi tool is limited to onl

[gmx-users] g_select help

Dear Gmxers, I did a simulation of 2048 liquid water and vapour interface using gromacs.I need to identify the dynamics of the molecules on the interface for which I am trying to use g_select but i am not sure how to go about it. In principle the box length along z-axis is 120 A and the interfac

[gmx-users] negative HB lifetime

Dear users, I try to calculate Hydrogen Bonding lifetimes with g_hbond, but I get a negative value for the forward time. I searched through the mailing list, and it reports that we should look to the ACF graph. In my case it falls dramatically to zero(I have attached it to this mail). How can I

Re: [gmx-users] How to do Monte Carlo in gmx

There will be no support for MC in GROMACS 5.0 Mark On Mon, Apr 14, 2014 at 4:20 PM, xiao wrote: > Dear Gromacs users, > > > I am studying the dimerization of two organic molecules. I hope i can > simulate the dimerization process by using Monte Carlo method. I noticed > that the MC script is

Re: [gmx-users] Determining interactions in Protein-Ligand complex simulations

On 4/14/14, 10:03 AM, MUSYOKA THOMMAS wrote: Dear users, I am doing a 10 ns protein-ligand simulation and would like to determine the hydrogen and hydrophobic interactions per each ns and the participating amino acid residues. How do I go about this? g_hbond and g_mindist, combined with sui

Re: [gmx-users] How to do Monte Carlo in gmx

On 4/14/14, 10:20 AM, xiao wrote: Dear Gromacs users, I am studying the dimerization of two organic molecules. I hope i can simulate the dimerization process by using Monte Carlo method. I noticed that the MC script is in the latest version of gromacs 5.0, but there is no such manual on t

[gmx-users] How to do Monte Carlo in gmx

Dear Gromacs users, I am studying the dimerization of two organic molecules. I hope i can simulate the dimerization process by using Monte Carlo method. I noticed that the MC script is in the latest version of gromacs 5.0, but there is no such manual on that, and the latest manual is 4.6. Can

[gmx-users] Determining interactions in Protein-Ligand complex simulations

Dear users, I am doing a 10 ns protein-ligand simulation and would like to determine the hydrogen and hydrophobic interactions per each ns and the participating amino acid residues. How do I go about this? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.groma

Re: [gmx-users] Position restraints and double precision

Thank you for your reply. I will look into freezegrps, it might be just what I need. Question 1) was more related to whether needing such large numbers might be indicative of a problem with my calculation, given that they are 5 orders of magnitude larger than the default. Of course I would exp

Re: [gmx-users] Position restraints and double precision

On 4/14/14, 8:45 AM, Miguel Caro wrote: Hi all, I am trying to do an MD simulation of a small hexagonal box where I need some of the atoms to stay fixed. This is because I am mixing ab initio and classical MD and some of the atoms in my system should remain within the configuration predicted b

[gmx-users] Position restraints and double precision

Hi all, I am trying to do an MD simulation of a small hexagonal box where I need some of the atoms to stay fixed. This is because I am mixing ab initio and classical MD and some of the atoms in my system should remain within the configuration predicted by DFT. As far as I know, GROMACS only

Re: [gmx-users] make_ndx, boolean operations

Yep, seems right. Mark On Mon, Apr 14, 2014 at 2:00 PM, Dr. Vitaly Chaban wrote: > seems I achieved that with > > 1 & ! 2 > > > > Dr. Vitaly V. Chaban > > > On Mon, Apr 14, 2014 at 1:52 PM, Dr. Vitaly Chaban > wrote: > > Hi Everyone - > > > > What is my command line if I need to exclude sites

Re: [gmx-users] make_ndx, boolean operations

seems I achieved that with 1 & ! 2 Dr. Vitaly V. Chaban On Mon, Apr 14, 2014 at 1:52 PM, Dr. Vitaly Chaban wrote: > Hi Everyone - > > What is my command line if I need to exclude sites belonging to group > #2 from group #1? > > Thank you. > > > Dr. Vitaly V. Chaban -- Gromacs Users mailing

[gmx-users] make_ndx, boolean operations

Hi Everyone - What is my command line if I need to exclude sites belonging to group #2 from group #1? Thank you. Dr. Vitaly V. Chaban -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read h