[gmx-users] gmx mdrun with gpu

Dear all, I want to run a simulation in gromacs 2019 on a system with 1 gpu and 32 threads. I write this command: gmx mdrun -s md.tpr -v -nb gpu but it seems it does not recognize gpus and it takes long for the simulation to reach its end (-ntmpi ntomp and nt seem not working either). In gromacs

Re: [gmx-users] gmx mdrun with gpu

Hello Reza Yes I complied it with GPU and the version of CUDA is 9.1. Any suggestions? Thanks. On Sat., May 4, 2019, 1:45 a.m. Reza Esmaeeli, wrote: > Hello Maryam, > Have you compiled the gromacs 2019 with GPU? > What version of CUDA do you have? > > - Reza > > On Saturday

Re: [gmx-users] best performance on GPU

ring service and post a link. > > Mark > > On Fri, 2 Aug 2019 at 01:05, Maryam wrote: > > > Dear all > > I want to run a simulation of approximately 12000 atoms system in gromacs > > 2016.6 on GPU with the following machine structure: > > Precision: single

Re: [gmx-users] best performance on GPU

what the problem is without more information. > > Please upload your .log file to a file sharing service and post a link. > > > > Mark > > > >> On Fri, 2 Aug 2019 at 01:05, Maryam wrote: > >> > >> Dear all > >> I want to run a simulation

[gmx-users] best performance on GPU

Dear all I want to run a simulation of approximately 12000 atoms system in gromacs 2016.6 on GPU with the following machine structure: Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD instructions: AVX2_256

[gmx-users] space dependent electric field

Dear all, I want to apply a space but not time dependent electric field to my system. I reviewed the source code of the electric field but it only has constant and time dependent EF (pulsed EF). Can anyone help me find out how I can change the source code to have space dependent EF without

[gmx-users] Time step mismatch.

this warning : Timesteps at t=1.4028e+07 don't match (1200, 1500), How do I fix this? is it possible to rewrite the time step after the simulation?Thanks in advance. Best regards, Maryam

[gmx-users] Converting Charmm to gmx format using cgenff

it with charm22* and did not get any error, I will just like to double check. Looking forward to your reply. Best regards, Maryam

[gmx-users] protein-cnt

I am doing simulation of the protein-cnt complex.How can I compute the protein-SWCNT interface area and interaction energy and heat capacity for cnt? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Interaction energy of system as a function of the interface area

Dear all My system consists of protein and CNT. I know I can calculate Interaction energy and interface area using g_energy and g_sas tools, respectively. I want to obtain Interaction energy of my system as a function of the interface area between the protein and CNT. How to do this? Any help

[gmx-users] interaction energy

Dear gromacs users My system contains protein and CNT and water molecules. I want to obtain interaction energy. There is following equation in some papers: E(int) = E(cnt+protein) - E(cnt) - E(protein). Based on this equation, should 3 MD simulations? 1- cnt in water 2- protein in water 3-

[gmx-users] Calculate heat capacity

Dear gromacs users My system contains protein(15 residue) and CNT and water molecules and ion. at the end of .top file is [ molecules ] ; Compound#mols Protein_chain_A 1 CNT 1 SOL 6531 NA 2 I want to calculate the heat capacity in

[gmx-users] Calculate heat capacity

Dear gromacs users My system contains protein(15 residue) and CNT and water molecules and ion. at the end of .top file is [ molecules ] ; Compound#mols Protein_chain_A 1 CNT 1 SOL 6531 NA 2 I want to calculate the heat capacity in

[gmx-users] how to calculate angles (molecules directions)

Dear users, Is there a way in GROMACS to calculate the angle of each molecule with a specified vector in each step? Thank you in advance. Regards, --Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Fwd: how to calculate angles (molecules directions)

Dear Christopher, I will try the ways you mentioned. One of them should work! I wanted a faster way than writing a code. However, if nothing works, I have to try programming.at last. Thanks a lot! Cheers, --Maryam On Fri, Feb 13, 2015 at 8:51 AM, Christopher Neale chris.ne...@alum.utoronto.ca

[gmx-users] Fwd: how to calculate angles (molecules directions)

-- Forwarded message -- From: Maryam Kowsar maryam.kow...@gmail.com Date: Fri, Feb 13, 2015 at 12:14 AM Subject: how to calculate angles (molecules directions) To: gromacs.org_gmx-users@maillist.sys.kth.se Dear users, Is there a way in GROMACS to calculate the angle of each

Re: [gmx-users] Fwd: how to calculate angles (molecules directions)

Dear Christopher, I tried g_traj -ox but it just gives me the positions not the orientations. I think I should try g_dipole. thank you very much! Cheers, --Maryam On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Maryam: I don't know. If g_dipoles

Re: [gmx-users] Epsilon-rf

If I use PME there's no need to find epsilon-rf, but I have to change some other parameters. I will try it. Thank you very much Alex! On Tue, Apr 28, 2015 at 11:31 AM, Alex nedoma...@gmail.com wrote: With reaction-field-zero, the only option is epsilon-rf=0. That aside, if the nanotube is

[gmx-users] Epsilon-rf

Dear all, I use reaction-field-zero as the coulombtype for my system. I wonder how I should choose the right epsilon-rf. How can I calculate the dielectric constant in the system? Thank you. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Epsilon-rf

as finding epsilon-rf in generalized field reaction? THANKS! On Tue, Apr 28, 2015 at 10:22 PM, Maryam Kowsar maryam.kow...@gmail.com wrote: If I use PME there's no need to find epsilon-rf, but I have to change some other parameters. I will try it. Thank you very much Alex! On Tue, Apr 28, 2015 at 11

Re: [gmx-users] filling a mesopore with water

Hi Chaban, they are less than 5 Angstrom. On Tue, Jun 23, 2015 at 1:30 AM, V.V.Chaban vvcha...@gmail.com wrote: what's the size of the hole? On Mon, Jun 22, 2015 at 11:37 AM, Maryam Kowsar maryam.kow...@gmail.com wrote: Dear users, I want to fill a mesoporous system with water

[gmx-users] filling a mesopore with water

Dear users, I want to fill a mesoporous system with water or any other molecules or atoms. I tested genbox -cp .gro -cs spc216.gro -o but water molecules only surround the mespore not in the holes. Are there any commands in gromacs? thank you. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] freezing graphene sheet

That's probably because of your forcefield. But if you want to freeze atoms or groups, you can simply do it by freeezgrps and freezedim in your .mdp file. In the former you should assign the groups you want to freeze and in the latter the directions, eg. 'Y,Y,Y' which means freezing in x,y and z

[gmx-users] uninstallation- removing unknown files from bin

Dear users, I want to uninstall gromacs. I used this command: rm -rf /usr/local/gromacs and also removed some links that began with g_*** in the bin . however, I'm not sure if the rest belong to gromacs or other programs also use them, and should be deleted or not: completion.bash,

[gmx-users] charge in *.n2t file

Hi Hassan, Charges depends on your system. You can find it either from the related articles or calculate it yourself. On Thu, Aug 13, 2015 at 11:08 AM, حسن هاشم زاده hashemzadehas...@gmail.com javascript:_e(%7B%7D,'cvml','hashemzadehas...@gmail.com'); wrote: hi all I use from charmm27.ff

Re: [gmx-users] force field

let me modify my previous message: in the g_x2top command, not grompp :-) On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar maryam.kow...@gmail.com wrote: Hi Mohammad, Yes that's possible. You should just have the necessary files of your desired forcefield(.atp,.itp,...), and put them

Re: [gmx-users] force field

is possible, provided you have parameters for such species. -Justin thank you, M. On Sunday, August 9, 2015 8:17 PM, Maryam Kowsar maryam.kow...@gmail.com wrote: let me modify my previous message: in the g_x2top command, not grompp :-) On Sun, Aug 9, 2015 at 8:14 PM, Maryam

Re: [gmx-users] force field

Hi Mohammad, Yes that's possible. You should just have the necessary files of your desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp command just add -ff folder name. that's all! It will use your forcefield instead of the present forcefields in gromacs. Regards, -Maryam

Re: [gmx-users] bonded parameter

Hi Hassan, For making a topology(.top) file all parameters of your forcefield is needed. On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده hashemzadehas...@gmail.com wrote: Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- Gromacs Users mailing

Re: [gmx-users] magnetic field - segmentation fault

Thank you Erik! On Sun, Jul 26, 2015 at 2:49 AM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Maryam, I usually like to keep it simple and use gdb. That said, clang+lldb is a great compiler+debugger combo. Valgrind may also be helpful. Kind regards, Erik On 24 Jul 2015, at 18

Re: [gmx-users] magnetic field - segmentation fault

wonder why you think it may cause problems. Velocities should change. I guess I can ask you questions then. Which version of gromacs are you working with? Which source codes have you modified? Thank you! On Fri, Jul 24, 2015 at 8:41 AM, Man Hoang Viet mhv...@ifpan.edu.pl wrote: Hi Maryam Kowsar

[gmx-users] magnetic field - segmentation fault

Dear users, Iam trying to add magnetic field code to gromacs. I think I did all the modifications necessary in all source codes but when I use mdrun command it gives me segmentation fault error while in md.log the magnetic field is present. When I change tpx_version the error is gone but in

[gmx-users] electric field

Dear users, I applied electric fields of different magnitudes (less than 1 v/nm since higher amounts are avoided) in my system. I have some charged water molecules and I expected to see very different results when the magnitude is changed, but haven't got that much difference. How can I be sure

Re: [gmx-users] electric field

field. > > Good luck! > > Viet Man > > > > Date: Sun, 15 Nov 2015 22:58:34 +0330 > > From: Maryam Kowsar <maryam.kow...@gmail.com> > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] electric field > > Message-ID: > >

[gmx-users] output control

Dear users, I have a simulation which lasts in 2ns and has around 4G trajectory if Iset nstxout = 1000. I need the output file of coordinates and velocities written every step which means a 4000G output file! Is there a way that I can manage the tarjectory so that only in the last 200ps of

Re: [gmx-users] output control

ring the 1.8 ns > and another of 200ps. Then you use different writing frequencies for the > two simulations. > > -- > P. > > Maryam Kowsar <maryam.kow...@gmail.com> a écrit : > > Dear users, >> >> I have a simulation which lasts in 2ns and has around 4G tra

Re: [gmx-users] output control

Thanks Mark and Pierre. I would rather try Mark's solution but I exactly dont understand what I should do now! I used 2 sets of commands tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt OR tpbcov -s -o new.tpr -extend 20 grompp -f

Re: [gmx-users] output control

Yes of course! That would be so kind of you to send the editor and a brief description of how it works. Thanks a lot tsjerk. On Monday, October 12, 2015, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Maryam, > > You only need a modified TPR file. There's no need to hassle wi

Re: [gmx-users] topology parameters

Thanks Vitaly! On Sun, Sep 6, 2015 at 3:29 PM, Vitaly V. Chaban wrote: > Bonded interactions are important. Sections are for human understanding. > > > > > On Sun, Sep 6, 2015 at 3:36 AM, mah maz wrote: > > Dear users, > > > > Are resnr, residue,

Re: [gmx-users] User-Specified LJ Epsilon and Sigma

Hi dan I think that's not possible to change forcefield parameters and use the old defined forcefield like opls. When you change the parameters in .itp you should introduce your own forcefield. Try to have all the needed files of forcefield in a new folder and use that during making topology. On

Re: [gmx-users] User-Specified LJ Epsilon and Sigma

gt; > On 9/9/15 7:29 AM, Maryam Kowsar wrote: > >> Hi dan >> I think that's not possible to change forcefield parameters and use the >> old >> defined forcefield like opls. When you change the parameters in .itp you >> should introduce your own forcefield. T

[gmx-users] New atom definition

Dear all, I want to use some atoms that are not implemented in gromacs. If i even make a .gro file, making a topology is a problem. What should i do? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] New atom definition

On 9/17/15 3:08 PM, Maryam Kowsar wrote: > >> Dear all, >> >> I want to use some atoms that are not implemented in gromacs. If i even >> make a .gro file, making a topology is a problem. What should i do? >> >> > Derive parameters in a manner consistent wi

[gmx-users] CNT in water

Dear Users, I want to simulate CNT in water solvent with CHARMM27 force field. The used parameters for simulation of CNT follows: The .n2t file is: CCA0.0012.011 3C 0.141 C 0.141 C 0.141 CCA0.0012.011 2C 0.141 C 0.141 The cntbonded.itp is: [

Re: [gmx-users] Extending simulations

Hi I think it should be like this: tpbconv -s previous.tpr -extend timetoextendby -o new.tpr mdrun -s new.tpr -cpi previous.cpt On Tue, Dec 22, 2015 at 2:07 PM, Mark Abraham wrote: > Hi, > > Please start with >

[gmx-users] electrostatic energy calculation

Dear all, I want to calculate the electrostatic energy (coulomb SR and LR) for a set of molecules during the whole simulation. I used g_energy -f ener.edr -o (with or without -nmol option), but it only gives me 1 average output for the last step.I tried g_enemat -f -etot (-emat) but it stops

[gmx-users] electrostatic energy calculation

opers would like me to make a Redmine.. > > >> > > >> > Hi there, > > >> > > > >> > g_energy or gmx energy just lists the short-ranged non-bonded > > >> potential > > >> > energies of those species w

[gmx-users] MSD

Dear all I want to calculate the MSD of a group of molecules in my system. In the .mdp file, xtc_grps is set for this group only. When I use g_msd - n -f -o (-mol does not work) and select the mentioned group, it stops after a while in the 2000th frame. Is there anything wrong with the

[gmx-users] rdf calculation with respect to center of mass

Dear gmx-users, The radial distribution function with respect to center-of-mass was computable in old gromacs versions. How can I calculate that  in newer version(2016)? Thanks in advance. Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Force field for ion-carbon interaction

Dear all What is the best and most proper force field for ions (like Na+ and Ca2+) and carbon structured systems interactions? I found a few papers which used Amber force field. Has anyone worked with or seen any papers in this regard? Thanks. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Force field for ion-carbon interaction

andard and well-tested description for > ions. > > Best of luck! :) > > Alex > > > On 12/21/2016 11:40 PM, Maryam Kowsar wrote: > >> Thank you Alex. Actually I used Amber since I havent found any better >> force >> fields for nonbonded interacti

[gmx-users] all electron force field

Dear all, I need to use a potential in which electrons are also considered for my simulations in Gromacs. I found the all-electron force field which is already implemented in Lammps package. Is it possible to use or implement it in GROMACS? Can i use QM/MM calculations in Gromacs instead? Also,

[gmx-users] Gromacs installation to do coupled QMMM with Gaussian

Dear all, How can I compile Gromacs for doing QMM/MM computations with Gaussian ? Is there a special flag during installation process? I have read the instructions in http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM But it is not a step by step instruction. Your help

[gmx-users] gromacs.org_gmx-users@maillist.sys.kth.se; jalem...@vt.edu

the same error while converting to str file... -- Maryam S. Sadeghi P *Please think before printing* -- 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

[gmx-users] Average RDF

e Oe-Ow RDF for each single O within the chain, but I am actually looking for the average RDF of all ether Oxygens. Could anyone tell me how I can compute an average RDF in GROMACS for all the ether Oxygens within the chain? Thank you Maryam -- Gromacs Users mailing list * Please search the arc

[gmx-users] Average RDF

each single O within the chain, but I am actually looking for the average RDF of all ether Oxygens. Could anyone tell me how I can compute an average RDF in GROMACS for all the ether Oxygens within the chain and O-water in 1 single graph? Thank you -- Maryam S. Sadeghi P *Please think before prin

[gmx-users] Iterative Boltzman Inversion

Dear All, I was wondering if there are any codes in GROMACS for doing Iterative Boltzman Inversion to reproduce the target pair distribution functions for a MARTINI coarse grained structure given by atomistic simulations? Best Maryam -- Gromacs Users mailing list * Please search the archive

[gmx-users] largest charge group

://www.gromacs.org/Documentation/Errors Could anyone suggest how I can fix this problem? I will need to do simulations on longer chains as well. Thank you Maryam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] largest charge group

Thank you very much Justin. Just to confirm, in case of longer polymers can I assign 1 monomer/bead to different charge groups? Maryam On Mon, Dec 30, 2019, 5:32 AM Justin Lemkul wrote: > > > On 12/30/19 2:53 AM, Maryam Sadeghi wrote: > > Dear All, > > > > I have

Re: [gmx-users] Scale Triclinic Box

parameters of the unit cell simultaneously while remaping the new coordinates inside the scaled cell... could "gmx genconf -nbox ... ... ..." handle this? Best Maryam On Fri, Apr 3, 2020, 2:54 PM Salman Zarrini wrote: > Hi Maryam, > > The ``gmx genconf -nbox 2 2 1'' is your

Re: [gmx-users] Scale Triclinic Box

. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, 340 angles and 376 dihedrals. Best Maryam On Sat, Apr 4, 2020, 4:54 AM Justin Lemkul wrote: > > > On 4/3/20 11:16 PM, Maryam Sadeghi wrote: > > Hi Salman, > > > > Tnx for the info, I actually want to do

[gmx-users] Scale Triclinic Box

Dear All, I need to scale the a and b parameters of a triclinic crystalline unit cell. When I use the editconf command, only the cell parameters are scaled while the coordinates of atoms are not remapped in the new cell. gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686

[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

Hi All, I have created a crystal structure of 2 polymer chains (PEG) and I need to calculate the cohesive energy for my system using CHARMM36 FF. In this case my fix_mol2 file includes 2 ligands, to convert to str file I get the following error: readmol2 warning: non-unique atoms were

[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

Hi All, I have created a crystal structure of 2 polymer chains (PEG) and I need to calculate the cohesive energy for my system using CHARMM36 FF. In this case my fix_mol2 file includes 2 ligands, to convert to str file I get the following error: readmol2 warning: non-unique atoms were