[gmx-users] UMBRELLA SAMPLING

Hi gromacs users, I want to perfom NVT equilibration, pull code (using pull-geometry = direction-periodic) Prior to this step, energy minimization (500 steps) and NPT equilibration (5 steps) was done As I am new to gromacs and simulations, can anyone tell me whether the following NVT

[gmx-users] UMBRELLA SAMPLING

Hi gromacs users, I want to calculate delta G for protein ligand binding. Had run the umbrella pulling simulation for 100 ps (protein ligand solvated in water), applying restraint in the protein (using the code in gromacs tutorial website, Bevenlab). But, after running the perl script

Re: [gmx-users] topology

Did you try PRODRG server? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of RAHUL SURESH Sent: Thursday, March 2, 2017 9:53 AM To: gmx-us...@gromacs.org Subject:

[gmx-users] HOW TO SPLIT RESIDUES

Hi gromacs users, How to split residue 2? Here, there are two identical organic compounds in water. Each compound has 29 atoms (consisting of carbon, nitrogen and hydrogen) Gave the command splitres 2. How to proceed after that? 0 System : 9664 atoms 1 Other :

Re: [gmx-users] ERROR IN BASH SCRIPTING

t by running the script through dos2unix. Next time, do that, or use an editor that comes from cygwin. Be sure you read things like https://cygwin.com/cygwin-ug-net/using-effectively.html so you understand your own tools. Mark On Tue, Feb 28, 2017 at 11:54 AM Subashini .K <subashi...@hotmail.co

Re: [gmx-users] ERROR IN BASH SCRIPTING

proper text editor next time ;-) Mark On Tue, 28 Feb 2017 08:14 Subashini .K <subashi...@hotmail.com> wrote: > Hi gromacs users, > > > I use the following run.sh in the working directory of simulations > > > #!/bin/bash > set -e > > for ((i=0;i<

[gmx-users] ERROR IN BASH SCRIPTING

Hi gromacs users, I use the following run.sh in the working directory of simulations #!/bin/bash set -e for ((i=0;i<27;i++)); do x=$(echo "0.05*$(($i+1))" | bc); sed 's/WINDOW/'$x'/g' mdp/min.mdp > grompp.mdp gmx grompp -o min.$i -pp min.$i -po min.$i -n index.ndx gmx mdrun

[gmx-users] TOPOLBUILD 1.3

Hi gromacs users, I want to use oplsaa force field for my organic compound. Can anyone tell me how to install topolbuild 1.3 and thereby generate .GRO, .ITP and .TOP with opls-aa parameter incorporated in it? Thanks, Subashini.K -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] deformation in simulation

Many tutorials suggest to run two equilibrations and then production file. At first, run a restrained equilibrium. Then non-restrained equilibrium followed by production file. Do not know the aim of your simulations. Hope this answer helps. Thanks, Subashini.K

[gmx-users] UMBRELLA SAMPLING

Hi gromacs users, I want to calculate the binding energy (ΔGbind) using umbrella sampling method (between protein and ligand which is solvated in water) How to custom index groups for the pulling simulation? The protein under consideration has only one chain A. Thanks, Subashini.K --

[gmx-users] PROTEIN-LIGAND SIMULATION

Hi gromacs users, In order to calculate binding energy of single protein inhibitor complex through simulations, how long should we run the calculations? Is 2ns sufficient? How to obtain results and plot time (in ps) along x-axis and binding energy (kJ/mol)along y-axis? Had completed two

Re: [gmx-users] DETECTING HYDROGEN BONDS

t each column is. If I recall correctly, the second column is the number of hbonds according to the default search cutoff. The first column is your simulated time in ps. Alex On 2/11/2017 1:00 AM, Subashini .K wrote: > Hi gromacs users, > > > After protein ligand simulations, gave the fol

[gmx-users] DETECTING HYDROGEN BONDS

Hi gromacs users, After protein ligand simulations, gave the following command to detect hydrogen bond gmx hbond -f npt.trr -s npt.tpr -num hbond.xvg After selecting protein and ligand Obtained the following result I am a beginner. Could someone help me to interpret these numbers? The

[gmx-users] ANALYSING PROTEIN LIGAND SIMULATIONS

Hi gromacs users, Have completed protein ligand simulations for 2 ns. How to view the position fluctuations of the ligand inside the protein and observe stable binding modes? How to extract useful information post simulations? Thanks, Subashini.K -- Gromacs Users mailing list *

Re: [gmx-users] Radial distribution function for larger distances

em is to get any useful suggestions. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Subashini .K <subashi...@hotmail.com> Sent: 08 February 2017 00:08:57 To: gmx-us...@g

[gmx-users] Radial distribution function for larger distances

Hi Gromacs users, How to calculate RDF for larger distances, say 15 angstrom using the following code. In which line should we focus to make changes? Can someone help? integrator = md dt = 0.002 ; 2 fs nsteps = 500 ; 10.0 ns

Re: [gmx-users] INDEX

dowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 6 Feb 2017, at 13:06, Subashini .K <subashi...@hotmail.com<mailto:subashi...@hotmail.com>> wrote: Hi gromacs users, I want to visualize th

[gmx-users] INDEX

Hi gromacs users, I want to visualize the results of simulations using the command gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb Wish to see Protein and ligand simulations together in the pdb file. But, when the command is given, we can either select protein group or ligand group

[gmx-users] PROTEIN LIGAND SIMULATION DYNAMICS

Hi Gromacs users, I am new to simulation dynamics. On what basis do we add water molecules to the protein ligand complex? Should we ensure that the system is fully solvated? Or, can we consider simulation without solvent (water molecules)? Thanks, Subashini.K -- Gromacs Users

[gmx-users] VISUALIZING PROTEIN FOLDING

Hi gromacs users, Through NVT equilibration, had obtained nvt.gro and nvt.trr. Are these files sufficient to visualize protein folding? What option in VMD has to be explored to observe protein folding? Thanks, Subashini.K -- Gromacs Users mailing list * Please search the archive at

[gmx-users] PROTEIN FOLDING IN GROMACS

Hi gromacs users, What are the steps for simulation to observe protein folding in gromacs? Thanks, Subashini.K -- 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

Re: [gmx-users] REGARDING TOPOLOGY FILE

ent: Thursday, January 19, 2017 12:40 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE can you please recognize that two extra atoms generated by acepype?? On Jan 19, 2017 4:00 PM, "Subashini .K" <subashi...@hotmail.com> wrote: > Thank you very

Re: [gmx-users] REGARDING TOPOLOGY FILE

and top file also check that the 2nd line in gro file showing the total number of atoms should be in parallel with all the atoms existed in the gro file this way you may solve the problem good luck On Jan 19, 2017 3:20 PM, "Subashini .K" <subashi...@hotmail.com> wrote: > Hi,

Re: [gmx-users] REGARDING TOPOLOGY FILE

1 On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashi...@hotmail.com> wrote: > Hi gromacs users, > > > Had taken one organic molecule (ligand) and many water molecules using > tleap of Amber tools 15. > > > Then generated .top and .gro file using acpype by the

[gmx-users] REGARDING TOPOLOGY FILE

Hi gromacs users, Had taken one organic molecule (ligand) and many water molecules using tleap of Amber tools 15. Then generated .top and .gro file using acpype by the command, acpype -p com_solvated.top -x com_solvated.crd -b ligand However, while using the same for gromacs, obtained the

[gmx-users] CLARIFICATION IN RESIDUE TOPOLOGY FILE

Hi gromacs users, While preparing the .rtp file, what does the third and fourth column describe? ; Methane [ CH4 ] [ atoms ] C opls_138-0.240 1 H1 opls_140 0.060 1 H2 opls_140 0.060 1 H3 opls_140 0.060 1 H4 opls_140 0.060 1

[gmx-users] PREPARING THE RESIDUE TOPOLOGY FILE

Hi, I am learning to prepare the residue topology file (.rtp file) . While preparing the file, what does the third and fourth column describe? This is the example of methane. What do the numbers -0.240 and 1 convey? Similarly 0.060 and 1? [ bondedtypes ] ; bonds angles dihedrals

Re: [gmx-users] converting pdb file to gromacs input file

add a hetatm in an existing force field.? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Subashini .K <subashi...@hotmail.com> Sent: Saturday, January 14, 2017 12:04:40 PM T

[gmx-users] converting pdb file to gromacs input file

Hi gromacs users, I am a new gromacs user. I wanted to generate a .gro, .itp, .conf file using the command $ gmx pdb2gmx -f lig.pdb However, the pdb file must be in the required format. What should we type instead of LIG corresponding to each and every atom? This is an example file of

[gmx-users] G_ENERGY COMMAND

Hi gromacs users, I am using gromacs in windows 7, 64 bit. When the following command was given, gmx g_energy -f ener.part0001.edr -o vol.xvg the error was GROMACS: gmx, VERSION 5.1.1 Executable: /usr/local/gromacs/bin/gmx.exe Data prefix: /usr/local/gromacs Command line: gmx

[gmx-users] REGARDING PROTEIN LIGAND SIMULATION

Hi gromacs users, I am working on protein-ligand simulation..The commands were given in the following order (1) source leaprc.ff14SB loadAmberParams frcmod.tip4pew loadAmberParams frcmod.ionsjc_tip4pew source leaprc.gaff LIG = loadmol2 LIG.mol2 loadamberparams LIG.frcmod check LIG receptor =

Re: [gmx-users] gromacs in cgywin

ot;. -- With my best wishes, Ming Li, PhD Chinese Academy of Agricultural Sciences, Beijing, China At 2017-01-11 16:24:16, "Subashini .K" <subashi...@hotmail.com> wrote: >Hi, > > >I have installed gromacs in cgywin. > >I want to run these commands > > &g

[gmx-users] gromacs in cgywin

Hi, I have installed gromacs in cgywin. I want to run these commands #em.mdp ; to test ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v ; mdrun -v -deffnm em I had sourced gmrx before typing these commands. source /usr/local/gromacs/bin/GMXRC But, it says, -bash: syntax

[gmx-users] GROMACS IN CGYWIN

11, 2017 12:30 AM To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] ENERGY MINIMIZATION Hi, In a cygwin terminal, having source'd GMXRC (see the install guide), just like you need to do under Linux. Mark On Tue, Jan 10, 2017 at 7:29 PM Subashini

[gmx-users] ENERGY MINIMIZATION

Hi Gromacs users, I have installed gromacs in windows 7, 64 bit using cgywin. I want to use the em.mdp file to grompp and generate a .tpr file. In which terminal should the following commands be executed? ; to test ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v ; mdrun -v

[gmx-users] Error in leaprc.ff14SB (Amber14)

Hi Gromacs users, While using the tleap of AmberTools 15, we give the following command source /home/admin/amber14/dat/leap/cmd/leaprc.ff14SB However, the following error is shown in cgywin command prompt -bash: logFile: command not found -bash: addAtomTypes: command not found -bash:

[gmx-users] HOW TO RUN GROMACS IN WINDOWS 7

Hi Gromacs users, I am new to Gromacs. Have installed it in windows 7. Had followed the instructions this website https://winmostar.com/en/gmx4wm_en_win.html How to run a test file through cygwin? Can someone help? Thanks, Subashini.K -- Gromacs Users mailing list * Please search the