[gmx-users] Information about different analysis tools in Gromacs

Dear Gromacs users, I just wondering about some source to get the detailed information about different analysis tools available in latest version of Gromacs. I have noticed that such informations about different tools are available in the old Gromacs manuals (For eg., Appendix D in Gromacs 4.6.7

Re: [gmx-users] Protocol for Gromacs analysis

properties of the membrane-protein system. Many thanks Anu On Wed, Mar 2, 2016 at 7:55 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Anu, > > With oligomers, sure. > > Cheers, > > Tsjerk > > On Wed, Mar 2, 2016 at 8:39 PM, anu chandra <anu

[gmx-users] Protocol for Gromacs analysis

Dear Gromcas users, I am quite new to Gromacs and I have just completed 100 ns simulation of a membrane protein using Gromcas. Now, I would like to do some basic analysis like RMSD, RMSF, Hydrogen bonding etc with the 100 ns trajectories. Below, I just wrote down the steps I adapted to generate

[gmx-users] Adding chain ID with g_cluster outputs

Dear Gromcas users, I have used g_cluster to do RMSD-based cluster analysis. Unfortunately, the generated center structures ( with option -cl) are failed to visualize with Pymol. I presume that one of the reason may be due to the lack of chain ID information in the the PDB as the protein is a

[gmx-users] Reading multiple trajectories for Gromacs analysis

Hello all, I just finished a 100 ns simulation using Gromacs, where I ran the simulation with a 5 ns window (ie. now I have 20 .trr files with 5 ns data in each). As I am quiet new to Gromacs, I just wonder how can I read all the 20 trr files one-by-one to do some basic Gromacs analysis. For e.g

[gmx-users] How to visualizing gro file in pymol

Hello all, I just finished a short simulation of a membrane protein system and trying to visualize the final gro file generated from the simulation using Pymol. Unfortunately, the Pymol failed to visualize the protein in cartoon representation. Though VMD can do the job, I just wonder is there a

[gmx-users] Simulation runs indefinitely

Hello Gromcas users, I having been simulating few membrane-protein systems for about ~300ns, using a 20 ns window for each run. Though I used the command ' gmx_mpi convert-tpr -s md20.tpr -f md20.cpt -e md20.edr -o md21.tpr -extend 2 ' to generate the tpr file for the next run, interestingly,

Re: [gmx-users] Simulation runs indefinitely

og > files to see what was different. > > Mark > > On Wed, Jan 27, 2016 at 1:46 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 1/27/16 6:28 AM, anu chandra wrote: > > > Hello Gromcas users, > > > > > > I having been simula

[gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations

Dear Gromcas users, I have been following the Gromcas tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/08_MD.html ) for setting up and running MD simulations of membrane proteins. I am aiming for a microsecond long simulation. In this regard, I

[gmx-users] Simulation terminated after 260 ns of simulation

Dear Gromcas users, I have been carrying out a simulation of protein in POPC membrane. After the successful completion of about 260 ns, simulation terminated with the following error. *** Reading checkpoint file 16md.cpt generated: Sun

Re: [gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories

treated gro file since, as you said, the same treatment with trjconv is required for coordinates in trr file. Many thanks Anu On Wed, Aug 19, 2015 at 12:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/19/15 7:22 AM, anu chandra wrote: Dear Gromacs users, I just noticed that during simulation

[gmx-users] A query about nsteps

Dear gromcas users, I carried out a continuation of previous md run for nsteps of 500 and dt of 0.002 using the following commands, gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi md1.cpt -deffnm md2 The mdp file following run

[gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories

Dear Gromacs users, I just noticed that during simulation 'mdrun' writes gro file in two formats - one with broken molecules at the boundaries and other one where surface molecules are perfectly wrapped. Interestingly, this difference in format depends on where I run the simulation - either in a

[gmx-users] Few queries about microsecond long simulations

Dear Gromcas users, I am planning to do microsecond long simulation of membrane-protein system and I have ~100,000 atoms in the systems. Since I am trying for microsecond long simulations and I have a quiet large system, it can generate large amount of data and in this regard I would like to

[gmx-users] Error: 'mdrun_mpi' is not a GROMACS command.

Dear Gromcas users, I just expericend an error while running mpi version of Gromcas on a 64 processors in a cluster. The command I used for running mdrun is as follows, mpirun -ppn 16 -np 64 gmx_mpi mdrun_mpi -cpi eq1.cpt -deffnm eq2 But, unfortunately the run terminated with following error

Re: [gmx-users] Error: 'mdrun_mpi' is not a GROMACS command.

Thanks Justin. On Tue, Aug 18, 2015 at 1:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/18/15 8:08 AM, anu chandra wrote: Dear Gromcas users, I just expericend an error while running mpi version of Gromcas on a 64 processors in a cluster. The command I used for running mdrun

Re: [gmx-users] Few queries about microsecond long simulations

as well. On Tue, Aug 18, 2015 at 4:30 PM, Felipe Merino felipe.mer...@mpi-dortmund.mpg.de wrote: Hi, This are all questions that mostly only you can answer. On 18/08/15 12:42, anu chandra wrote: Dear Gromcas users, I am planning to do microsecond long simulation of membrane

[gmx-users] Difference in molecule wrapping in gro file

Dear Gromacs users, I just noticed that the gro file written from simulation carried out in Dell cluster and my local desktop workstation have difference in warping the molecules. In server, following grommp and mdrun commands are used, gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t

Re: [gmx-users] log file not writing simulation time in continuous manner

Dear Justin, Thanks a lot for your prompt reply. On Sat, Aug 15, 2015 at 2:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/15/15 9:51 AM, anu chandra wrote: Dear Gromcas users, I have used grompp, as shown below, to generate .tpr file in order to continue the simulation. gmx_mpi

Re: [gmx-users] Distance restrain with dummy atom

** Can you please help me to figure out what is going wrong with the position restraint and simulation? Many thanks in advance Anu On Wed, Aug 12, 2015 at 12:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/11/15 11:06 AM, anu chandra wrote: Dear Justin, Thanks

[gmx-users] Distance restrain with dummy atom

Dear Gromacs users, I am working with membrane simulations and I would like to put distance restrain along Z-axis between a dummy atom I generated at the centre of box and all the water molecules. For this, I first generated a dummy atom at the centre of box and also made a simple .itp file for

Re: [gmx-users] Distance restrain with dummy atom

= com Many thanks Anu On Tue, Aug 11, 2015 at 3:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/11/15 8:30 AM, anu chandra wrote: Dear Gromacs users, I am working with membrane simulations and I would like to put distance restrain along Z-axis between a dummy atom I generated

[gmx-users] Warning with ewald-geometry = 3dc

Dear Gromcas Users, I am trying to run membrane protein simulation with slab geometry and EW3DC method (ewald-geometry = 3dc). As mentioned in the article http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0 , I have set up my system with extended Z-dimension and used pbc =

[gmx-users] Hole in the membrane during initial equilibration

Dear Gromacs users, I am trying to run a membrane protein simulation with slab geometry along Z-axis, due to ion asymmetry. The simulation box was well equilibrated before implementing the slab geometry. The box dimension before the addition of slab was - ' 112.347 112.347 126.531 90.00

[gmx-users] mdp file for slab geometry

Dear gromacs users, I am planing to run a membrane protein simulation with implementation of a slab geometry, due to ion asymmetry. Below, I just copied the mdp file that I will be using for NPT equilibration and later, for production run. Can you please have a look and let me know if there is a

Re: [gmx-users] Position restraining of ions.

), as they need to be listed in the same order in the [ molecules ] table. Gordan On 7/16/2015 2:36 AM, Justin Lemkul wrote: On 7/15/15 11:53 AM, anu chandra wrote: Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain

Re: [gmx-users] Position restraining of ions.

Thanks for the reply. I have one more quick query about position restrain here and its about restraining some pat of the whole protein. Say, I have a protein of 400 aminoacinds ( ie., residues no. 1-400). I would like to set up position restrain in such way that backbone atoms of residues 101-200

[gmx-users] Position restraining of ions.

Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f

Re: [gmx-users] Ions moving to the opposite layer during minimization.

). What all modification I should make in mdp input file to take care of the slab geometry? Many thanks in advance Anu On Tue, Jul 14, 2015 at 3:57 PM, anu chandra anu80...@gmail.com wrote: Thanks for the reply Mark. Yes, its a periodic box. Below is the input mdp I have used for minimization

[gmx-users] pdb2gmx error with addition of terminal group

Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have downloaded Gromacs compatible Chamrmm36ff from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the N-terminal acetyl (ACE) and C-terminal

Re: [gmx-users] pdb2gmx error with addition of terminal group

Thanks Justin. Its working fine. On Wed, Jul 8, 2015 at 12:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/8/15 6:39 AM, anu chandra wrote: Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have

Re: [gmx-users] Gromcas tools listing with 'gmx'

, Jul 6, 2015 at 5:36 PM anu chandra anu80...@gmail.com wrote: Dear Gromcas users, I have installed latest version of Gromcas and while using I am adding 'gmx' prior the all the Gromacs tools ( for eg, pdb2gmx). Unfortunately, the 'TAB' key failed to list the possible commands if I

Re: [gmx-users] Gromcas tools listing with 'gmx'

, Jul 7, 2015 at 11:54 AM anu chandra anu80...@gmail.com wrote: Hi, Thanks for the reply. Sorry if I didn't make my query clear. When I use gm and then TAB, it gives me all choice of commands that start with gm, that include gmx also. But, when I do TAB after gmx space pdb2, it list

Re: [gmx-users] Missing terminal cap group

/User_contributions/Force_fields ) with the one from MacKerell lab? Many thanks Aneesh On Fri, Jul 3, 2015 at 4:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/3/15 11:10 AM, anu chandra wrote: Dear Gromacs users, I am trying to generate topology for a membrane protein, which is capped with acetyl

Re: [gmx-users] Topology for ready-made membrane protein system

Dear Justin, Do I need to add lipid topology manually, if I use Charmm36 force filed that have protein and lipid parameters together? Thanks Anu On Fri, Jul 3, 2015 at 4:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/3/15 7:56 AM, anu chandra wrote: Dear Gromacs users, I am working

[gmx-users] Gromcas tools listing with 'gmx'

Dear Gromcas users, I have installed latest version of Gromcas and while using I am adding 'gmx' prior the all the Gromacs tools ( for eg, pdb2gmx). Unfortunately, the 'TAB' key failed to list the possible commands if I use 'gmx' prior to any Gromacs tools.This leaves me each time to remember

[gmx-users] Missing terminal cap group

Dear Gromacs users, I am trying to generate topology for a membrane protein, which is capped with acetyl and methyl amide group, using Charmm36 force field in Gromacs. Unfortunately, the acetyl (ACE) group is seems to be missing in the Gromacs Charmm36 force field. Can anybody suggest me a way to

[gmx-users] Topology for ready-made membrane protein system

Dear Gromacs users, I am working with membrane proteins. I have generated the membrane-protein system ( contains lipids, protein, water and ions) with some specification. For eg., I have positioned few ions and water molecules at particular location using some in-house programs. Now, I would

[gmx-users] Topology for ready-made membrane protein system

Dear Gromacs users, I am working with membrane proteins. I have generated the membrane-protein system ( contains lipids, protein, water and ions) with some specification. For eg., I have positioned few ions and water molecules at particular location using some in-house programs. Now, I would

[gmx-users] Adding ions to membrane protein system

Dear Gromacs users, I am working with membrane proteins. I have build my membrane-protein systems with a layer of water bed on top and bottom of the membrane. Now, I would like to add a specific concentration of KCl to bottom layer of the water bed. Can anybody suggest me a way to add ions to a

Re: [gmx-users] membrane model

really wish to use it to build your membrane system (I have done this before for converting DPPC/POPC membranes to a range of different united-atom force fields). Cheers Tom On 19/06/15 15:53, Justin Lemkul wrote: On 6/19/15 10:52 AM, anu chandra wrote: Dear Gromacs users, I am

[gmx-users] membrane model

Dear Gromacs users, I am planing to do a protein simulation in acyl chain united-atom POPC membrane model. It will of great help if few of my queries regarding setting up the system get answered. 1. Which force filed will be suitable for united atom (acyl chain) POPC? Will CHARMM36 have united

Re: [gmx-users] membrane model

the all-atom POPC model. Many thanks Anu On Fri, Jun 19, 2015 at 3:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/15 10:52 AM, anu chandra wrote: Dear Gromacs users, I am planing to do a protein simulation in acyl chain united-atom POPC membrane model. It will of great help if few