Re: [gmx-users] Scale Triclinic Box

Hi Maryam, The ``gmx genconf -nbox 2 2 1'' is your friend to generate a supercell, I am just not sure if it could handle a triclinic cell. Since your unit cell is not that large, you even can use Avogadro or ASE-gui which both are good molecule editors and visualizers. Cheers, Salman On Fri,

Re: [gmx-users] writing trajectory of an atom

file. Do you have any idea for that? > > Thanks > Hadi > > Sent from my iPhone > > > On Dec 17, 2019, at 5:37 PM, Salman Zarrini > wrote: > > > > Hi Haid, > > > > In your index file, you should first generate a group which contains only > &

Re: [gmx-users] writing trajectory of an atom

Hi Haid, In your index file, you should first generate a group which contains only the atom of your interest: gmx mak_ndx -f case.gro -o index.ndx > a atom > q Then you can extract the trajectory of that single group (single atom) using: gmx trjconv -f traj.xtc -n index.ndx -o

Re: [gmx-users] Radial Density Profile

Hi Elham, In general to calculate the radial density profile of a droplet-like object one should do binning (histogram) in spherical coordinate along radius. That means you should define a series of shell each with thickness of dr and all centered on center of the vesicle. And then you could

Re: [gmx-users] Iterative Boltzman Inversion

Hi Maryam, If I am not wrong, VOTCA-CSG (http://www.votca.org) is the package that might help you. It parameterizes course-grained potentials based on structural properties of the system using different approaches including the iterative Boltzman Inversion (iBI). All the GROMACS files can be

Re: [gmx-users] Flat-bottomed Restrain

a reference coordinate by which you dictate the desired molecule to move around the axes at (3.0, 3,0) as much as 1.5 nm while the molecule is free to move along the Z as much as it likes. Regards, Salman Zarrini On Tue, Jul 16, 2019 at 1:03 PM ehsan shahini wrote: > Dear Salman, > &g

Re: [gmx-users] Flat-bottomed Restrain

1AMNA C10*5* *3.000 3.000* 4.390 ... (rest of the unrestrained atoms) ... (rest of the unrestrained atoms) ... (rest of the unrestrained atoms) ... (rest of the unrestrained atoms) I hope it works! Cheers, Salman Zarrini On Tue, Jul 16, 2019 at 4:58 AM Mark Abraham

Re: [gmx-users] Self-interaction across periodic boundaries

. Best regards, Salman Zarrini On Mon, Jul 8, 2019 at 6:24 AM Mark Abraham wrote: > Hi, > > If you're trying to model something like it was at infinite dilution using > a periodic box, then the size of the box needs to be at least as large as > the size of the structure an

[gmx-users] Self-interaction across periodic boundaries

percolating aggregates in which the molecules are self-interacting across the periodic boundaries. I wonder if there is any possibility to prevent aggregates self-interaction across periodic boundaries? Thank you, Salman -- Best regards, Salman Zarrini -- Gromacs Users mailing list * Please

[gmx-users] Gyration tensor

Calculate the radii of gyration about the principal axes. Dear all, The -p flag in gmx gyrate would calculate the radii of gyration about the principal axes, Rga, Rgb and Rgc. I wonder what the relation between the eigenvalues of diagonalized gyration tensor and what we get here in Gromacs as

[gmx-users] Memory corruption by malloc()

to the gmx density! Anyway, please find the error file below, any hint would be highly appreciated. https://drive.google.com/open?id=1GYdymvAa_d2UZ2hXV1GZs2tyRG06-Gwb Regards, Salman Zarrini P.S. Gromacs version: 2018.2 and 2018.6 -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] perl water_deletor.pl

Hi On Fri, Jan 18, 2019 at 3:30 AM rabee khorram wrote: > *Hello everyone, * > *I am running liposome structure with gromacs 5.* > *this liposome created with Packmol software(without water molecules).* > *after Solvating liposome with water in gromacs, I need to remove waters > from hydrophobic

[gmx-users] Conversion CHARMM FF to Gromos54a7 FF

Dear all, I have a CHARMM all atoms force fields for a solid with limited atom types, and I want to convert them to Gromos54a7 force fields. Would you please confirm that below are the changes I should make to do so? 1. Combination rule # 2 is used in CHARMM whereas GROMOS which uses # 1, so, In

[gmx-users] Dihedrals/Impropers

Dear all, I wonder if it is necessary to list all the Dihedrals/Impropers of the molecule in a MD simulation? If not so, what kind of Dihedrals we don't need to list? Thank you. Regards, Salman -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] GROMACS- MAGNETIC FIELD

Hi, Magnetic fields interact with the electronic/atomic's spin which plays no role in the Newton’s equations governing in classical mechanics and molecular dynamics. While the electric fields interact with the atomic charge which represent itself in coulomb interaction. Regards, Salman On Thu,

[gmx-users] Topology file

Dear all, I want to create a topol.top file for Silica slab for which the force fields parameters are available in literature as well as in the lammps.data file which works fine in lammps (below links). The slab has in general 2184 atom including two types of O atom(OS in surface part and OB in

Re: [gmx-users] HB analysis at surfaces

If you mean water profile density then "gmx density" is your friend. Just invoke below command and play around with the variables to reach your desire. gmx density -f case.trr -s case.tpr -n index.ndx -d Z -dens mass -o WD.xvg -b 1 -sl 5000 Cheers, S.Zarrini On Fri, Jan 27, 2017 at 5:18

Re: [gmx-users] PMF decompostion

? Thanks, Salman Zarrini On Mon, Dec 5, 2016 at 12:07 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/3/16 10:29 AM, Salman Zarrini wrote: > >> Thanks David and Christopher for your responses. >> >> I do not understand why vdW and Q are not meaningful co

Re: [gmx-users] PMF decompostion

nalyzing and fitting are "non-mass wighted" in my calculations. Do you think I should get something close to the entropy of the quasihamonic approximation Schlitter's formula if I use the method proposed by you? Cheers, Salman Zarrini On Sat, Dec 3, 2016 at 7:19 AM, David van der Spoe

[gmx-users] PMF decompostion

or in my case solid surface-water interaction, will be taken into account automatically when one calculates the PMF in aqueous solution in gromacs? Thanks. Cheers, Salman Zarrini -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX