Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

Hi Mark, I starting converting from AMBER (according to the paper) to GROMACS and comparing the results. Please explain in more words what this constant of two mean or how can I handle it. Ignoring it and just converting the units, I got these results AMBER (table 2a) Rmin/2 (Å) epsilon

Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

On 4/21/16 4:30 PM, Pedro Lacerda wrote: Hi Mark, I starting converting from AMBER (according to the paper) to GROMACS and comparing the results. Please explain in more words what this constant of two mean or how can I handle it. Ignoring it and just converting the units, I got these results

[gmx-users] Catenation and Visualization

Hello everyone I have completed two independent 100 ns simulations of two differnt proteins in water. One is monomer and the other is trimer. Both simulations were allowed to run for 50 ns intially, after visulation, trajectories were 'correct' and then extended the simulation to 100 ns. Now

Re: [gmx-users] Installation Problem... No command 'gmx' found

Thanks everyone. For your quick reply and support. On Thu, Apr 21, 2016 at 10:37 PM, Justin Lemkul wrote: > > > On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote: > >> Hi, in my case gmx is only needed for certain commands. For example >> pdb2gmx is working if I use it

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

Hi Stéphane, Did you see the following or similar output from running /path/to/cuda/samples/1_Utilities/deviceQuery/deviceQuery when GROMACS wasn't able to detect GPU? ./deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned

[gmx-users] Volume of system

hi Gmx experts i want to calculate Volume corresponding to the one molar standard state. is there any tool in gromacs to do that. i read about gmx density. Background: i have Protein-ligand complex simulation and i need to find energy of restraints which requires Volume. Thanks in advance

Re: [gmx-users] empty index group

On 4/21/16 7:29 AM, David Newman wrote: Hi, So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom index of a binding pocket on my protein of interest, I want to group 5 non-contiguous residues, I can index them separately and tried to group them with & but that creates

Re: [gmx-users] sugar puckering

Le 21/04/2016 04:24, bharat gupta a écrit : Dear Gmx Users, I am interested in calculating cremer-pople parameters for a trisachharide ligand from its simulation docked with a protein. I found one tool g_puckering for calculating the parameters but it was written for Gromacs version 4.0.x and I

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

On 4/21/16 6:57 AM, Tuhin Samanta wrote: please check it... [ moleculetype ] ; molname nrexcl HOD 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_116 1HOD OW 1 -0.8476 2 opls_117 1HOD HW

[gmx-users] empty index group

Hi, So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom index of a binding pocket on my protein of interest, I want to group 5 non-contiguous residues, I can index them separately and tried to group them with & but that creates an empty group error because I guess it

Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is working if I use it solo, not with gmx. It's worth a shot. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on

Re: [gmx-users] Installation Problem... No command 'gmx' found

On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote: Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is working if I use it solo, not with gmx. It's worth a shot. This is true for versions in the 5.0.x series; they can be called via gmx or through the old

Re: [gmx-users] Moving this mailing list to Discourse format

Hi Mark, many thanks. At the end it is really just a question if the user has flexibility over how to visualise the communications. I'm happy to hear that the old-fashioned email way would still have (some) support :-) I hope you get sufficient feedback and support from the community. Cheers,

Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi, Try gmx [command] . Ex. gmx mdrun -option Regards, Husen > On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote: > > Hi, > > Try gmx_mpi. > > Regards > Terry > > >> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir >> wrote: >> >> Dear all user >>

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

On Thu, Apr 21, 2016 at 3:54 AM, treinz wrote: > Hi, > > > Can you also explain why the function calls to cudaDriverGetVersion() and > cudaRuntimeGetVersion() both return 0, as in Not really, but it is the normal behavior on hosts where the runtime is not compatible with the

[gmx-users] vdwradii issue

Dear Gmx-Users Currently i'm having this kind of sticky warning when i am doing gmx solvate or gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my working directory, or use -vdwread flag still get this warning..Please how to get rid off of this Warning!    WARNING:

[gmx-users] vdwradii issue

Dear Gmx-Users Currently i'm having this kind of sticky warning when i am doing gmx solvate or gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my working directory, or use -vdwread flag still get this warning..Please how to get rid off of this Warning!    WARNING:

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 119

Hi, Indeed, Link atoms have to be added to the .gro file. The atom indexing in the .gro file is not used, so no need to renumber. A simple editconf can do that for you if too, if you would like to have the numbering correct. However, you need to adjust the total number of atoms at the top of

[gmx-users] Number of urea molecules for 2.1 M solution

Dear all, How to calculate number of urea molecules required for a box size of 294.68 nm^3 for 2.1 M urea solution regds Divya -- 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

[gmx-users] Moving this mailing list to Discourse format

Hi people, As part of the new BioExcel project (http://bioexcel.eu/) that supports biomolecular research with codes including GROMACS, we're exploring migrating the gmx-users mailing list to the Discourse format. You can see an example at http://try.discourse.org! This has a number of immediate

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

The topology file for my system - HOD System like that --- #include "oplsaa.ff/forcefield.itp" ; Include hod topology #include "hod.itp" [ system ] ;Name HOD [ molecules ] ; Compound#mols HOD102 .mdp file is like that - (FOR Energy minimization) ;

Re: [gmx-users] Moving this mailing list to Discourse format

On Thu, 21 Apr 2016 07:11:42 + Mark Abraham wrote: > Hi people, > > As part of the new BioExcel project (http://bioexcel.eu/) that > supports biomolecular research with codes including GROMACS, we're > exploring migrating the gmx-users mailing list to the Discourse

[gmx-users] NA or SOD in CHARMM36

Hi all, I'm trying to simulate a protein-ligand complex in POPC membrane using the CHARMM36 forcefield, which I got from the Mackerell site and included in /share/gromacs/top/. Now when I run grompp I get the error "Fatal error: No such moleculetype SOD" despite the fact that I have #include

Re: [gmx-users] NA or SOD in CHARMM36

On 4/21/16 4:56 AM, Jason Loo Siau Ee wrote: Hi all, I'm trying to simulate a protein-ligand complex in POPC membrane using the CHARMM36 forcefield, which I got from the Mackerell site and included in /share/gromacs/top/. Now when I run grompp I get the error "Fatal error: No such

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

On 4/21/16 3:32 AM, Tuhin Samanta wrote: The topology file for my system - HOD System like that --- #include "oplsaa.ff/forcefield.itp" ; Include hod topology #include "hod.itp" [ system ] ;Name HOD [ molecules ] ; Compound#mols HOD102 .mdp file is

Re: [gmx-users] Number of urea molecules for 2.1 M solution

On 4/21/16 3:00 AM, Divya Dube wrote: Dear all, How to calculate number of urea molecules required for a box size of 294.68 nm^3 for 2.1 M urea solution You have a volume, you have a desired concentration, C = n/V. -Justin -- == Justin A.

Re: [gmx-users] trouble with ca2+ atom and SEP recognition in Gromacs 5.1.1

On 4/20/16 3:56 PM, Jayant James wrote: Hi! All I have been running into some trouble with CA2+ recognition in GMX 5.1.1. So some back ground..I have a protein that I am trying to simulate that has three chains.First chain is 161 amino acids long, second one is about 200AA and the third

Re: [gmx-users] Defining LA atoms in .gro file

Dear GMX Users, I am trying to perform QM/MM simulation for my system and I need to define LA for the boundary between QM and MM region. I have the boundary regions but I don't know how to add them in the gro file. Do I have to manually modify the .gro file, if that's the case, adding, them

Re: [gmx-users] Moving this mailing list to Discourse format

Hi Hannes, Yes, previous discussion has identified this as a likely key feature, and thanks for adding confirmation of that. Discourse can be integrated with functionality for replying to threads from email to suit people who want that kind of small change to their workflows; that will indeed

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

please check it... [ moleculetype ] ; molname nrexcl HOD 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_116 1HOD OW 1 -0.8476 2 opls_117 1HOD HW 1 0.4238 3 opls_805 1HOD