[gmx-users] Gromacs mdrun for k20 and cpu

Hi to all, im new to gromacs, Im performing Tutorials my system has 2 x Intel® E5-2650V2 Processor (8Core) +2 GPU (Tesla k20 and Gt 610) installed gromacs GPU version and total 16 core and 32 threads available in proc. please share me the command to use both gpu and processor for MD (mdrun

[gmx-users] including .itp file to system

Hello everyone, i wanted to perform a Protein-Ligand Simulation,i created .itp,psf,.par etc files for ligand and am able to make topol.top and conf.gro or the protein using pdb2gmx .Forcefield is CHARMM27 Now i im confused how to include ligand into my system.as per tutorial we are provided with

[gmx-users] Regarding .itp file to the system

Justin, Thanks for your quick reply so how i should proceed with .itp file as per your tutorial .gro file is required ,if i add "new.itp" to topol.top there might be problem that atom number mismatch between the conf.gro which produced for protein alone When i tried to load mol2 file in charmmgui

[gmx-users] Regarding .itp file to the system

Dear Justin, Thanks for your previous answer i quoted below "1. Process the protein with pdb2gmx and obtain a .top and coordinate file in whatever format you like. 2. Generate a ligand topology, #include its .itp file in the .top 3. Append the ligand coordinates to those of the protein from step

[gmx-users] Forcefiled

Dear all, When we select a United atom ff and When we select All atom forcefield,is it depends on the number of amino residues? what difference it will make in either cases (looking for any link or source where i can find the details ) and regarding the selection of any force filed i have seen

[gmx-users] Protein Ligand simulation

Greetings to all ! i have completed Protein Ligand simulation as per the tutorial,my aim to proof that ligand A inhibit Ligand B -what are the possible analysis i can perform i have done the following RMSD - to see the stability of protein with ligands RMSF-root mean square deviation of

[gmx-users] Protein Ligand simulation

Greetings to all ! i have completed Protein Ligand simulation as per the tutorial,my aim to proof that ligand A inhibit Ligand B -what are the possible analysis i can perform i have done the following RMSD - to see the stability of protein with ligands RMSF-root mean square deviation of

[gmx-users] gmx cluster

Dear gmx experts, I would calculate to energetically favoured conformation of my ligand with protein for 100ns MD traj. I guess I have to use gmx cluster ,Any assistance on how to proceed . I need to get at least 10 most favoured conformations. gmx cluster -f input.xtc -s input.tpr -method

[gmx-users] permeation events- ion channels in bilayer

Dear GMX users, We are looking for water permeation events across the ion-channel, which is embedded in lipid bilayer. After one micro second MD simulation in Gromacs2016.1 i used the below script for calculating the permeation events, http://www.ks.uiuc.edu/Training/Tutorials/science/

[gmx-users] Heavy metals parameterisation

Dear Gromacs users, I would like to study heavy metals (cadmium, mercury, lead, Arsenic, platinum and Chromium) interaction with proteins using charm36 ff. Where and how I can get parameters for these heavy metals ions.? If it is not available where i should start, to develop the parameters for

Re: [gmx-users] Heavy metals parameterisation

Thanks, In general for parameterising the small molecules or heavy metals VMD- FFTK is sufficient? or is there any other tools I need to use other than the Gaussian package (for DFT or MP2). -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Heavy metals parameterisation

Thanks Justin, I am looking for the effect of heavy metals in channel proteins. Could you please provide me some links or paper to where i can start QMMM. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Heavy metals parameterisation

Dear Justin, More specifically, I'm looking for the transport properties of proteins in presence and absence of heavy metals- how heavy metals affecting the transportation of molecules across the channels. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Heavy metals parameterisation

I'm looking something like this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856166/ Here the mercury bind to Cys residue and inhibiting the channel. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] domain decomposition error

Dear all gromacs users, I have seen in mail archive this domain decomposition error can be avoided with less number of processor, but how to find the suitable number of processor required? here is the log file. ​​ https://drive.google.com/file/d/0Bzs8lO6WJxD9alRTYjFaMjBTT2c/view?usp=sharing --

Re: [gmx-users] Terminal group patching

Hi, How to find the in the most realistic way? When i tried to build a protein-membrane system using charmm-gui there were two options First is GLYP and ACE and for last there was options like CTER CT1 CT2 CT3 NONE which one i should select? How do i know which one -- Gromacs Users mailing

[gmx-users] Terminal group patching

Dea gromacs users, Is it necessary we have to do terminal group patching before doing MD simulation? Can anyone tell me why it is required or what will happen if we don't do it? any information or source of information is appreciated. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] domain decomposition error- ------

Dear all gromacs users, I have seen in mail archive this domain decomposition error can be avoided with less number of processor, but how to find the suitable number of processor required? here is the log file. ​​https://drive.google.com/file/d/0Bzs8lO6WJxD9alRTYjFaMjBTT2c/ view?usp=sharing --

Re: [gmx-users] pulling of a molecule through protein-membrane system

Dear Justin, Well, Charmm-gui not providing an option to make a long box in one direction. So is it fine increasing the box and adding the water in Charmm-gui output pdb file and proceed? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] positioning molecule at desired location

Dear all, I want to keep a water molecule at a particular position of a protein channel. I need to pull this across the channel and observe the energy diagram by PMF. can anyone tell me how I can keep water molecules at a particular position. thank you. -- Gromacs Users mailing list * Please

Re: [gmx-users] simulation at different temperature

Dear Justin, Thanks for the reply, Could you tell me what is the unique purpose of the REMD and where I can learn it from basics? -- 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] Simulation ended prematurely, no performance report will be written- Minimization

Dear all, I'm trying to minimise the CGMD system and end up with an error Steepest Descents converged to machine precision in XX steps, but did not reach the requested Fmax < XX. I tried double precision and feed the *.gro file as the initial structure but the result was same. There were no

Re: [gmx-users] simulation at different temperature

Dear Alex, I guess this is annealing and which will give only one output.xtc, I'm looking for full dynamics of the system (say 100 ns for each temperature, 300 K,305 K340 K ). Further, I need to compare the results with each other. Thank you. -- Gromacs Users mailing list * Please search

[gmx-users] simulation at different temperature

Dear gmx users, I would like to see the temperature dependence of an ion channel/membrane protein in lipid bilayer system. My plan is to run a simulation at 300 K to 340 K by increasing 5 K and observing the permeation of molecules, pore diameter, sec structure .etc. Are there any techniques

[gmx-users] pulling of a molecule through protein-membrane system

Dear all gromacs users, I would like to build a protein-membrane system to perform umbrella simulation; I need to calculate the molecule transportation by pulling it from top to bottom. In the tutorial, it says "Some force fields include everything you need. For instance, it is unwise to try to

[gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

Dear all, In order to obtain the PMF diagram of a water molecule through membrane protein channel, I set up a simulation system and try to run with pull_coord1_geometry= direction-periodic. To correct te error following changes are made in the mdp file {error (Can not have dynamic box while

Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

Thank you very much, It worked with NVT, but the water molecule is not going though the channel at 0.01 nm per ns but It worked when i increased the pull_coord1_rate to 0.5 nm per ns from 0.01nm per ns but could not get proper histogram and energy profile. What parameters i need to change in

[gmx-users] CGMD with cut-off Verlet?

Dear all, While running CGMD in GPU i got this error OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet Here can i change the cut-off scheme to Verlet ? ff is martini22p -- Gromacs Users mailing list * Please search the

[gmx-users] CG MD

Dear all, I was wondering the analysis we usually use in the all-atom simulation will work in for CG model? I guess secondary structural analysis will be useless since it's not considering all atoms. What about non-bonded energies and other parameters such hydrogen bond and essential dynamics?

Re: [gmx-users] CG MD

>though most atomistic properties can be studied by rebuilding the atomistic coordinates from the CG. Various methods exist to >do this. Could you please provide a link to any material or paper for this. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] CGMD with cut-off Verlet? production run stage

Hi, Based on this mdp http://cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp i got NOTE You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. Is this something i need to consider or just ignore? --

[gmx-users] FEP: mdp setting for mutation

Hi, Following changes are made in the mdp file for mutation analysis.Can anyone tell me is there anything wrong here? ; init_lambda_state0123456789 10 11 12 13 14 15 16 17 18 19 20 vdw_lambdas = 0.00 0.05 0.10 0.15

Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

Dear Justin, As per the manual i have changed parameters as tcoupl = berendsen tc_grps = Protein Non-Protein Chain_B tau_t = 1.01.01.0 ref_t = 310 310 310 ; pcoupl = berendsen pcoupltype

[gmx-users] pull distance vs direction?

Hi to all, Is there any theoretical difference between pull_coord1_geometry= distance pull_coord1_geometry= direction (distance vs direction) other than simple distance pulling and pulling in specific direction.? I used to pull "distance" for a water molecule to transport through the

[gmx-users] Fixing dssp images using m2p file

Dear Gromacs experts, Which option i need to use to correct the dssp image as given in the link. (i have to get full part upto 100 ns in the box) You can see the right side is not full in the box, i marked in the black box

[gmx-users] tilt angle between the axis of a protein normal to the membrane

Dear gromacs users, I would like to calculates the tilt angle between the axis of a protein (its a nanotube, embedded perpendicular to the lipids-along z) and the normal to the membrane . I have used gmx gangle -f XXX.xtc -s XX.tpr -g1 vector -g2 z -oav angle.xvg, is it correct approach? --

[gmx-users] Gromacs FEP tutorial

Can anyone tell me which thermodynamics cycle was used in the tutorial? for FEP. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] Gromacs FEP tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html > -- 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] simulating glass materials using GROMACS

Dear experts, I would like to simulate NASICON type glass using GROMACS. The paper I referred to here used LAMPP (https://pubs.acs.org/doi/abs/10.1021/jp5094349). How should I proceed for this kind of study with GROMACS? What kind of forcefield I can use in GROMACS? can anyone provide a starting

[gmx-users] How to add osmotic stress

How to introduce osmotic stress on a simulation system to study the transportation differences in varying conditions.( protein-membrane system) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?