[gmx-users] Problems with non standar residue combining Amber and GAFF

Dear Gromacs users, I am trying to add a new residue into a peptide composed of standar residues. For that I have used Antechamber to get a starting topology for that residue, obtained the corresponding .itp file in GROMACS (using amb2gmx.pl) and then modified the corresponding files in

[gmx-users] problem with intermolecular restraints

Dear Gromacs users, I am trying to do a MD simulation using Gromacs 5.1 and intermolecular restraints. I have an DNA, two peptides, a linker and a Ni2+ ion, and I am trying to impose intermolecular distances for the coordination of the Ni2+ ion with the nitrogen atoms of the linker and of the

Re: [gmx-users] restraints between two different molecules

rom: mark.j.abra...@gmail.com > Date: Wed, 25 May 2016 14:19:26 + > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] restraints between two different molecules > > Hi, > > On Wed, May 25, 2016 at 4:11 PM Rebeca García Fandiño <rega...@hotmail.com> > wrote: &g

[gmx-users] g_covar error in Gromacs 5

Hi, I am trying to use g_covar like this: echo 2 2 | g_covar -s prod_clus_1_exp.tpr -f prod_clus_exp_fit.xtc -n index_noH_exp.ndx -o eigenval_300K_exp.xvg -v eigenvect_300K_exp.trr In Gromacs 5.0.4 I get an error: (...) Choose a group for the least squares fit Group 0 ( System)

Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS

org > From: jalem...@vt.edu > Date: Thu, 3 Sep 2015 16:37:18 -0400 > Subject: Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS > > > > On 9/3/15 3:40 PM, Rebeca García Fandiño wrote: > > Dear GROMACS users > > > > I have a general doubt >

Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS

rk you linked to, Angel Pineiro (who is also at USC) made this > (although if I remember correctly it was pretty slow in calculating the > order parameters). I'm sure he'd be happy to share, if you so wished. > > Cheers > > Tom > > On 03/09/15 21:37, Justin Lemkul wrote

[gmx-users] Reliability about Lipid Order Parameters in GROMACS

Dear GROMACS users I have a general doubt about the reliability of calculating order parameters for lipids containing saturated and unsaturated chains. For example, DOPC (attached). The order parameters for the two chains are too similar and however one of them is saturated and the other one

Re: [gmx-users] element symbol column in a pdb using editconf

://redmine.gromacs.org/issues/1307 and I can take a look? Mark On Tue, Jul 7, 2015 at 5:19 PM Rebeca García Fandiño rega...@hotmail.com wrote: Hi Mark, I just tried both proposals: 1) gmx editconf -f input.tpr -o output.pdb Where output.pdb is: (...) ATOM 1 C MOL 1

Re: [gmx-users] element symbol column in a pdb using editconf

work for you, but might not be convenient. I suspect gmx trjconv -s topol.tpr -f input.gro -o output.pdb might use the fixed machinery and do what you want. Mark On Tue, Jul 7, 2015 at 4:42 PM Rebeca García Fandiño rega...@hotmail.com wrote: Sorry, I did not mention because

[gmx-users] element symbol column in a pdb using editconf

Dear Gromacs users, I am trying to obtain a pdb file, using editconf, with the element symbol column. Looking for that, I found this revision: http://redmine.gromacs.org/issues/1307 It seems to be resolved, however, I am using GROMACS 5.0.4 and it is not working. Is there any way to retain

[gmx-users] mdrun domain decomposition in GROMACS 5 and GROMACS 4

Dear Gromacs users, I am trying to carry out a mdrun simulation (mdrun -v -deffnm prod ) and depending on the version and on the number of processors I use, I am having these errors: 1) Using GROMACS 5.0.4 (AMD architecture) and 2 or 4 processors, the calculation is OK. 2) Using GROMACS 4.6.2

[gmx-users] trjorder time-consuming

Dear GROMACS users, I am using the command gmx trjorder with a single frame of a trajectory, to order the water molecules according to the smallest distance to a molecule. The system is very small (4400 atoms), however gmx trjorder is taking more than 1 hour to finish!! Is it normal to be so

[gmx-users] no output for rmsd-dist.xvg in g_rms

Dear GROMACS users, I am trying to calculate the file rmsd-dist.xvg using g_rms and GROMACS 5.0.4 g_rms -s ../minimizado.tpr -f ../production_300K_vac_all_fit.xtc -o rmsd.xvg -dist rmsd-dist.xvg However, any file is generated with that option, only rmsd.xvg. Is is maybe a bug, or how could I

[gmx-users] value for epsilon_rf in a vacuum simulation

Dear GROMACS users, I am trying to carry out a simulation in vacuum (or gas phase). I have doubts about the proper values for epsilon_rf. I have found examples where this value is set to 78 http://www.shourjya.thinkbiosolution.com/md-simulation-in-gas-phasevacuum-with-gromacs/

[gmx-users] lost information box after g_cluster

Dear Gromacs users, when I use g_cluster -f trajectory.xtc -s topology.tpr -g clusters.log -cl clusters.pdb -cutoff 0.05 (...) the obtained file clusters.pdb does not contain any information about the box. I have tried with .gro, and also with the option of g_cluster -pbc, but the dimensions of

[gmx-users] trjcat with settime option using command line

Dear GROMACS users, I am trying to concatenate several trajectories with identical times using the command trjcat with the options -cat and -settime. I have to introduce manually the option c each time a new trajectory is read. I would like to introduce this line into a script, in such way I

[gmx-users] fixed number of clusters from a MD simulation

Dear Gromacs users, I am trying to find a method to obtain a fixed number of clusters (using g_cluster) from a MD simulation. The search of clusters is very manual, depending a lot of the cutoff selected for the analysis. Is there any way to calculate a fixed number of clusters from a MD

[gmx-users] coarse-grained topology for vitamin E

Dear Gromacs users, I am looking for a coarse-grained structure and the corresponding CG topology of vitamin E for simulating it using GROMACS. Does anyone know where could I get it? Thanks a lot for your help in advance. Best wishes, Rebeca. Dr. Rebeca Garcia Santiago de Compostela University

Re: [gmx-users] different mdrun errors in different machines

-architecture is the one that fails. :-( Cheers, Rebeca. Dr. Rebeca Garcia Santiago de Compostela University Date: Thu, 5 Mar 2015 07:53:56 -0500 From: jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] different mdrun errors in different machines On 3/5/15 7:45 AM, Rebeca García

[gmx-users] different mdrun errors in different machines

Dear GROMACS users, I am carrying out a MD simulation in GROMACS, and I am having problems in the mdrun step. We have tried it in two different machines: -The first of them is a 64 bytes system. There is no problem at all in this machine. -However, in another machine of 32 bytes system, mdrun

[gmx-users] solvate with an exact number of solvent molecules

Garcia Santiago de Compostela University Spain Hi Rebeca, In GROMACS 5.0, I use gmx insert-molecules -f your.gro -ci your_insert.gro -o output.gro -nmol xxx where xxx is the number you want. Hope it helps. Jennifer On Mon, Mar 2, 2015 at 6:44 PM, Rebeca García Fandiño regafan at hotmail.com

[gmx-users] solvate with an exact number of solvent molecules

Dear GROMACS users, I am trying to do a systematic study using GROMACS and I would like to have the same number of solvent molecules in all my systems. Using gmx solvate in GROMACS 5.0 it is only possible to select the maximum number of molecules in the box, but not a concrete number. Does

Re: [gmx-users] GAFF and alkynes (Justin Lemkul)

Hi, sorry for insisting about this issue...but it is not clear for me yet. I have increased (in 10 times) the force constant of the two angles involved in my molecule (those involving the alkyne) and I obtain a correct geometry without no errors during the simulation, and perfectly linear. Is

[gmx-users] GAFF and alkynes

Dear Gromacs users, I am trying to simulate an organic molecule containing an alkyne, using GROMACS and the GAFF force field. When I do grompp I get this note, referring to the atoms involved in the triple bond: NOTE 1 [file ligando_gmx.top, line 289]: The bond in molecule-type solute

Re: [gmx-users] GAFF and alkynes

Thanks a lot for the suggestions, Justin. In your CO2 tutorial I have seen the comment One cannot effectively build this molecule in the traditional sense, as there are algorithmic reasons why an angle of 180° is not stable during a simulation. I was wondering what happens if I use angle

[gmx-users] Changing atom names from pdb to gro in editconf

Dear Gromacs users, a general question about editconf... When I convert a pdb with 4 letters in the atom names into a gro file, the atom names change. For example, a pdb of the type: TITLE Great Red Owns Many ACres of Sand REMARKTHIS IS A SIMULATION BOX CRYST1 30.000 30.000 30.000

[gmx-users] recovering topology from tpr

Dear Gromacs users, Is it posible to recover the topology files (itp or top) from a binary tpr file? I have tried using this script: https://pythonhosted.org/MDAnalysis/_modules/MDAnalysis/topology/TPRParser.html However, the itp file seems a single line like this: {'_bonds': [(0, 3), (0, 7),

[gmx-users] charmm to gromacs

Dear Gromacs users, I am trying to obtain the .itp files for an organic molecule for a MD simulation in GROMACS using the CHARMM force field. I am trying to use cgenff_charmm2gmx.py: python cgenff_charmm2gmx.py MOL1 ligand.mol2 ligand.str charmm36-nov2014.ff After this step, I obtain several

[gmx-users] charmm to gromacs

Dear users, I am trying to generate .itp files for simulating a small molecule in GROMACS using the CHARMM force field. Starting from a pdb, and using MATCH MATCH.pl -forcefield top_all36_cgenff test.pdb I obtain 3 files: test.rtf, top_test.rtf and test.prm From these files, I would like to

[gmx-users] simulation in implicit solvent for non standar residues

Hi, I am trying to do a MD simulation in GROMACS of two non standar molecules using implicit solvent. Using explicit solvent I could do the simulation without problem using AMBER-GAFF or CHARMM-CGenFF parameters. To prepare the simulation in implicit solvent, I can see in the manual that a

[gmx-users] from amber to opls

Hi, I have done a simulation of an organic molecule (a cyclodextrin) using GAFF/AMBER parameters, and I would like to compare the results using another force-field (OPLS or CHARMM). Is there any direct way to go from the topology for AMBER to the topology for OPLS or CHARMM? Thanks a lot for

[gmx-users] 2D PMF for two ions

Hello, I am trying to carry out a 2D PMF calculations of two ions in a peptidic channel using GROMACS (and Umbrella Sampling). I have several technical questions: -Should I consider pull_ngroups= 3 (two of them ions and the other one the channel)? -Or should I carry out a 1D PMF for one

[gmx-users] SDS parameters

Hello, I am trying to found AMBER or GROMACS/AMBER parameters for SDS (sodium dodecyl sulphate). I have seen some papers simulating SDS with the Amber force field, but I have not found nor the parameters for SDS included by default in AMBER, neither any .top and .crd for the topology

[gmx-users] SDS parameters

Hello, I am trying to found AMBER or GROMACS/AMBER parameters for SDS (sodium dodecyl sulphate). I have seen some papers simulating SDS with the Amber force field, but I have not found nor the parameters for SDS included by default in AMBER, neither any .top and .crd for the topology anywhere.