Re: [gmx-users] Fw: asking guidance

Add the -sep flag that will split the writting into multiple files instead of 1 large pdb. Alternatively you could script up a spliting program with something like awk awk 'BEGIN{filename="MyFile_"i".pdb"}{print $0>filename; if $0~/ENDMDL/; i++;filename="MyFile_"i".pdb"}}' -Micholas

[gmx-users] computation/memory modifications

Hi, I want to do some tests on the lysozyme tutorial. Assume that the tutorial with the default parameters which is run for 10ps, takes X seconds wall clock time. If I want to increase the wall clock time, I can simply run for 100ps. However, that is not what I want. I want to increase the

[gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

Hello everyone, This question may be very simple to most of the Gromacs user. I wonder if Gromacs allow us to use both user-defined non-bonded potentials (Table potential) as well as Gromacs predefined potential at the same time. For example, if I have a system with a solute in a solvent and for

[gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA

Dear all, I am constructing a top file for gramicidin A a short that contains a succession of D- and L-AAs (the exact sequence is HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH) and have a unexpected problem whenI use charmm36 . Indeed

[gmx-users] dipole moment for one residue of the whole protein

Dear users, I want to calculate Phenyl dipole moment from my traj.trr file but my trajectory does not contain mass and charge. I used "gmx dipole " command for this purpose but it gives me error that Phenyl is not a whole molecule (actually because it is part of my protein which is a molecule

Re: [gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA

On 3/9/18 6:55 AM, ABEL Stephane wrote: Dear all, I am constructing a top file for gramicidin A a short that contains a succession of D- and L-AAs (the exact sequence is HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH) and have a

Re: [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs

Hi Mayank, Umbrella sampling replica exchange is currently not implemented in GROMACS. -- Viveca On Thu, Mar 8, 2018 at 5:32 PM, Mayank Dixit wrote: > Dear Gromacs Users, > I would like to calculate the potential of mean force between sodium and > chloride ion pair

Re: [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs

You could compile Gromacs with PLUMED (http://www.plumed.org/) and use that to run your umbrella sampling with replica exchange. -Marc On Thu, Mar 8, 2018 at 11:32 AM, Mayank Dixit wrote: > Dear Gromacs Users, > I would like to calculate the potential of mean force

[gmx-users] Fw: asking guidance

Dear director,I am using Gromacs package to perform MD simulations and I have a 100 ns long MD simulation. For the further assays, I must split this 100 ns trajectory into 100 pdb files (to get one pdf file from each 1000 ps or 1 ns of simulation). I have found two commands:  gmx trjconv -s

Re: [gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA

OK thank you Justin for the confirmation Stéphane -- On 3/9/18 6:55 AM, ABEL Stephane wrote: > Dear all, > > I am constructing a top file for gramicidin A a short that contains a > succession of D- and L-AAs (the exact sequence is >