[gmx-users] comm-mode option for applied external electric field.

Hi, I am trying to understand the comm-mode option in .mdp. I am simulating a DNA protein system with electric field. Now, if I understand correctly the comm-mode option, if I set it to linear, and comm-grps to System, it will remove the velocity of COM velocity of the system. But here I want to

[gmx-users] Problem in velocity plot while doing MD simulation of DNA protein with E field

? Thank you in advance, Regards, Arnab Mukherjee -- 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 (un)subscribe requests visit https://mai

Re: [gmx-users] Position restraints while performing pulling run for Umbrella sampling

Hello everyone, I hope I have been able to write it clearly the problem I am facing. It would be very helpful for me if someone can please guide me how to solve this problem. Thank you in advance, Regards, Arnab On Thu, Dec 20, 2018 at 8:20 PM ARNAB MUKHERJEE wrote: > Hi, > > I am

[gmx-users] Position restraints while performing pulling run for Umbrella sampling

Hi, I am intending to perform pulling run for umbrella sampling, on my coarse grained DNA protein system where I have a bundle containing 20 DNAs and proteins. I want to pull 1 DNA out of this bundle to perform Umbrella Sampling. I was going through this tutorial

[gmx-users] Position restraints with Martini force field

Hi everyone, I am simulating a DNA protein system with Martini forcefield. I want to use position restraints on all DNA atoms. So I used gmx genrestr command to generate .itp file for position restraints of all the DNA atoms. So without including position restraints, my .top file looks like this

Re: [gmx-users] Problem during equilibration using semi-isotropic pressure coupling

Hi Justin, Thank you very much for your reply. I would try also position restrain instead of freezing. But it is still strange to me why I got average pressure of 1 bar after running only for 5 ns for the completely frozen finite DNA when I did isotropic pressure coupling. But for the infinite

[gmx-users] Problem during equilibration using semi-isotropic pressure coupling

Hi everyone, I have a system of infinite CG (Martini) DNA (length of the DNA same as length of the periodic box) protein system. I am trying to equilibrate this system to 1 bar pressure. Since my DNA is same as the size of the box, I don't want the box to fluctuate along Z direction. Hence I am

Re: [gmx-users] Problem while equilibrating system with frozen groups

ng position restraints? Why not > let the loose entirely? Freezing creates large artefacts. > > Second, 4 ns equilibration is *way* too short. > > Lastly, see http://www.gromacs.org/Documentation/Terminology/Pressure > > > Peter > > > On 10-09-18 19:01, ARNAB MUKHERJ

[gmx-users] Problem while equilibrating system with frozen groups

Hi, I am simulating DNA (infinite) protein Martini system with electric field. I have 2 systems, for 1 complete DNA is frozen and for the 2nd one, only 4 atoms of the DNA is frozen. When I perform NPT equilibration for the complete DNA frozen system, it shows me this error : Fatal error: 4442

Re: [gmx-users] Cannot compute velocity of COM of a group of atoms

.mdp file), and compute the velocity for the old trajectory (.trr) file, rather than running a new simulation again? Thanks and Regards, Arnab On Wed, Aug 8, 2018 at 4:15 PM, Justin Lemkul wrote: > > > On 8/7/18 1:47 PM, ARNAB MUKHERJEE wrote: > >> Dear all, >> >> I ha

[gmx-users] Cannot compute velocity of COM of a group of atoms

Dear all, I have simulated a system of DNA and Protein, and I want to calculate the velocity of the center of mass of protein as a function of time. So I used the following command : gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov test-vel.xvg -com I have pasted below the file

[gmx-users] Error : symtab get_symtab_handle 367 not found

ank you in advance, Regards, Arnab Mukherjee -- 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 (un)subscribe requests visit ht

[gmx-users] Error : symtab get_symtab_handle 367 not found

ank you in advance, Regards, Arnab Mukherjee -- 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 (un)subscribe requests visit ht

[gmx-users] Error : symtab get_symtab_handle 367 not found

ank you in advance, Regards, Arnab Mukherjee -- 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 (un)subscribe requests visit ht

[gmx-users] Problem to compute interaction energy between different groups

nks in advance, Thanks and Regards, Arnab Mukherjee -- 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 (un)subscribe requests visit ht

[gmx-users] Freeze a group of atoms in gromacs

? Thanks a lot, Regards, Arnab Mukherjee -- 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 (un)subscribe requests visit https

[gmx-users] Having WCA bonded interaction with FENE potential

potential. But is there an easier way to do this? As FENE potential is already there as one of the bonded interactions in gromacs. Thanks a lot, Regards, Arnab Mukherjee -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Cosine bending potential

Hi, What is the function no. (funct) for the functional form of the bending potential U_bend = k_theta*(cos theta - cos theta_0)^2 ? Thanks and Regards, Arnab -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before