[gmx-users] (no subject)

Dear Justin its your conversation regarding pulling of dsDNA. Because gromacs is replying as there message is too big so cant be send and due to that I can not replied in orginal conversation. But I want to start from the last conversation. from your side "It seems to me you have two steps to

[gmx-users] Using different sets of parameters with the same functional form for a single dihedral

Hello Group, I want to define dihedral potential for a particular dihedral in GROMACS. My problem is that i have eight sets of parameters with *different multiplicity (n)* and f*orce constant value (k)* for the same dihedral of *functional form 1*.

Re: [gmx-users] energy minimization

Look around atom 2016, there is a bad contact between the atoms in that area, hence the infinite force, very high potential energy, and the minimisation fails. On Tue, 25 Sep. 2018, 6:48 pm ikjk, <1761440...@qq.com> wrote: > hello >I am doing a md with martini force filed,I create a box,

Re: [gmx-users] g_mindist error "Cannot open file with NULL filename string"

Hi, That looks like some kind of bug in mindist. Does an earlier version work for you? Are you able to upload a report for us at https://redmine.gromacs.org? Thanks Mark On Tue, Sep 25, 2018 at 3:30 PM ABEL Stephane wrote: > Hi All, > > I would like to use g_mindist (vGMX2018.2) to compute

[gmx-users] Topology file.

Hello everyone I use Gromacs 18.3. when I use the command "gmx pdb2gmx -f protein.pdb -o protein.gro" it makes a topology file. But this topology haven't "posre_Chain _A.itp" or any other posre in part "; Include chain topologies" im confused, that what is wrong?! Do I can add this posre parts

[gmx-users] g_mindist error "Cannot open file with NULL filename string"

Hi All, I would like to use g_mindist (vGMX2018.2) to compute the number of total contacts between each residue of a protein and surfactant molecules. For this I use the following command gmx_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n MYNDX.ndx -b 20 -e 215000 -dt 4 -d 0.4 -respertime

Re: [gmx-users] GROMACS/CPMD QMMM do not occur the process of the hydrogen abstraction reaction (limingru)

Hi, For such specific questions, it will be better to directly contact the authors of that study. Since the paper is not too long ago yet, they might share their input files with you. Good luck, Gerrit Dear all, I'm doing the QMMM simulation about OH radicals interacting with DNA's

[gmx-users] GROMACS/CPMD QMMM do not occur the process of the hydrogen abstraction reaction

Dear all, I'm doing the QMMM simulation about OH radicals interacting with DNA's base (Guanine) by using GMX-CPMD package. Based on the paper "Multiscale QM/MM Molecular Dynamics Study on the First Steps of Guanine Damage by Free Hydroxyl Radicals in Solution (web site:

[gmx-users] energy minimization

hello I am doing a md with martini force filed,I create a box, there is a double monolayer, then I solvate it, but when I did energy minimization, gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr then NOTE 1 [file minim.mdp]: With Verlet

[gmx-users] GROMACS/CPMD QMMM do not occur the process of the hydrogen abstraction reaction

Dear all, I'm doing the QMMM simulation about OH radicals interacting with DNA's base (Guanine) by using GMX-CPMD package. Based on the paper "Multiscale QM/MM Molecular Dynamics Study on the First Steps of Guanine Damage by Free Hydroxyl Radicals in Solution (web site:

Re: [gmx-users] secondary structure analysis

by using only the .gro is it possible to calculate the secondary structure of protein.because when i am using this comment do_dssp -s aa_charmm-eq.gro -n ../index-p.ndx -sss scount-p-0-1.xvg -o ss-p-0-1.xpm the error is Can not open file: traj.xtc because i have the all atom gro file (obtained by