[gmx-users] genion problem with topology

that the topol.top adds CL at the end under [molecules] but when I try to minimize the geometry using the new solvate.gro file the error as given as ERROR 1 [file topol.top, line 37]: No such moleculetype CL I do not understand how I can rectify the problem. Can someone help? *Thank you* *Gangotri

Re: [gmx-users] conversion of a trajectory from .trr to .gro

* On Mon, Sep 18, 2017 at 7:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/18/17 4:18 PM, gangotri dey wrote: > >> Hello! >> >> I would save it in vmd all at once but I would like to ideally save it in >> separate files. Also, the trajconv sta

Re: [gmx-users] gmx_mpi command line in version 5.1.4

I hope your gromacs is compiled in a parallel cluster for you to use gmx_mpi. *Thank you* *Gangotri * On Tue, Sep 19, 2017 at 11:06 AM, K. Subashini wrote: > Hi gromacs users, > > > I am using version 5.1.4 > > > How to use gmx_mpi? > > > I got the following error

Re: [gmx-users] conversion of a trajectory from .trr to .gro

load data and show the trr or xtc file. > right click on to it and save coordinate. File type. gro. > or > trajconv -f xxx.trr or xtc -s xxx.tpr -o xxx.gro > > RC Dash, > > > On Mon, Sep 18, 2017 at 2:42 PM, gangotri dey <holyriv...@gmail.com> > wrote: > >> Dear

[gmx-users] conversion of a trajectory from .trr to .gro

Dear all, I would like to transform my trajectory file n.trr or n.xtc to n.gro after my production run. I have used trjcat and trjconv to transform it using the index file. But in both the cases, it says "Can not write a gro file without atom names". How can I transform it please? *Thank you*

[gmx-users] easy sampling of data

Dear all, I have a simulation that I ran for 5 ns. I have saved after every 0.1 ps. I would like to extract the structure after every 1 ns. Is there any easy way to do it in gromacs? *Thank you* *Gangotri Dey* -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] (no subject)

this done as desired. If the question and the problem are not very clear, please let me know. I will try to reframe my words. Looking forward to a healthy discussion. Thank you G. *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology

Re: [gmx-users] (no subject)

you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Mon, Aug 7, 2017 at 5:04 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Are you tryi

[gmx-users] solvate only in the z-direction

Dear all, I am working with MnO2 surface and I would like to solvate the surface only in the z-direction. How best can I do it, please? *Thank you* *Gangotri Dey* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] (no subject)

gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= 18; generate a random seed *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick

[gmx-users] MnO2 periodic system

distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= 18; generate a random seed *Thank you* *Gangotri Dey* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] Problem with dihedral restraints

Thank you for the kind reply. I will compute and update in the post. *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Fri, Aug 4, 2017 at 10:31 AM, Mark

[gmx-users] Problem with dihedral restraints

-84.24 0 100 702698716712 150.3766 0 100 695691692702 1 -166.8294 0 100 My .mdp file is similar to the one used in the Bevan lab tutorial online. *Thank you* *Gangotri Dey* -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] segmentation fault for unknown reason

you* *Gangotri Dey* -- 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://maillist.sys.kth.se/mail

Re: [gmx-users] protein -ligand complex dissociating during simulation

Hey! You might want to constrain the bond between the 2 protein chains. G *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Fri, Jul 21, 2017 at 8:56 AM

[gmx-users] dihedral restraint

the previous version in the mdp file. However, the dihedral angles are changing and I am not sure how to restrain them. Is there any part that I am missing. *Thank you* *Gangotri Dey* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX