[gmx-users] Separate structure from box

Hi, I want to extract a structure in a box, i mean i want to extract a sheet from the box of solution, because i dont have any separated .gro file from my sheet. How can i do that? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] error in grompp step

Hi, You should probably also avoid using software that is five years old and no longer supported with bug fixes... Mark On Tue, Mar 20, 2018 at 6:09 AM Upendra N wrote: > Dear Justin sir, > > Thank you very much I tried that also but same errors were coming. > > I will try it out again si

Re: [gmx-users] nve energy conservation

Hi, On Mon, Mar 19, 2018 at 10:08 PM Jo wrote: > Hello, > > Thank you for your response. I have found a way to conserve energy of my > box of SPC/E water by removing 'settles' from my topology file. > Thus your water is no longer rigid. > Previously, the total energy of the system was consis

Re: [gmx-users] error in grompp step

Dear Justin sir, Thank you very much I tried that also but same errors were coming. I will try it out again sir With Regards Upendra N -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Topol file for a bigger system

On 3/19/18 8:15 PM, Alex wrote: Dear all, Using topolbuild I can generate the case.gro, case.top, ffcase.itp and posrecase.itp out of a case.mol2 which contain only a single molecule of X. Also, using the "gmx insert-molecules" I can generate a bigger system containing 1000 molecule of X, for

[gmx-users] Topol file for a bigger system

Dear all, Using topolbuild I can generate the case.gro, case.top, ffcase.itp and posrecase.itp out of a case.mol2 which contain only a single molecule of X. Also, using the "gmx insert-molecules" I can generate a bigger system containing 1000 molecule of X, for example to have case-1000.gro. Now

Re: [gmx-users] nve energy conservation

Le 19/03/2018 à 22:25, Jo a écrit : 3. It appears that having constraints explicitly defined in the topology file results in no energy conservation. Can someone explain to me why this might be? Dear Jo, Considering specifically this point, I suspect that your contraints are "added twice", onc

Re: [gmx-users] nve energy conservation

On 3/19/18 5:25 PM, Jo wrote: I just want to clarify my questions: 1. Does running the simulation with NO 'settles' and NO 'constraints' defined in the topology file, just 'bonds' and 'angles', give an accurate system of rigid SPCE water? No, exactly the opposite. Bonds and angles are modele

Re: [gmx-users] nve energy conservation

I just want to clarify my questions: 1. Does running the simulation with NO 'settles' and NO 'constraints' defined in the topology file, just 'bonds' and 'angles', give an accurate system of rigid SPCE water? 2. I am not sure how to define 'bonds' and 'angles' in the topology file that is rigid -

Re: [gmx-users] nve energy conservation

Hello, Thank you for your response. I have found a way to conserve energy of my box of SPC/E water by removing 'settles' from my topology file. Previously, the total energy of the system was consistently increasing or decreasing by a significant amount resulting in no energy conservation. I have

Re: [gmx-users] Free Energy solvation generate multiple dhdl.xvg output files

It sounds like you are only running one free energy simulation. You need to run one simulation for each lambda (changing "init-lambda-state" in your mdp file) and name the dhdl xvg file a different name for each one. On Mon, Mar 19, 2018 at 8:30 AM, Javier Luque Di Salvo < jluquedisa...@gmail.com>

[gmx-users] Error in grompp step

Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp and cordinates)

Re: [gmx-users] error in grompp step

On 3/19/18 10:05 AM, Upendra N wrote: Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp

[gmx-users] error in grompp step

Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp and cordinates)

[gmx-users] error in grompp step

Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp and cordinates)

[gmx-users] Free Energy solvation generate multiple dhdl.xvg output files

Dear Gromacs users, I am trying to run Free Energy calculations of a single ion in water (to calculate its solvation energy). Since this is a new topic for me, I am following the tutorial 'Solvation free energy of ethanol' (easily find in google). The three steps work well without erros (1-energy m

Re: [gmx-users] Structure factor and scattering intensity in gromacs 5.1.4

See the manuals for gmx sans and gmx saxs. Try at least doing a search for the answer to you question before posting. On Mon, Mar 19, 2018 at 10:08 AM, Rakesh Pant < rakesh.p...@students.iiserpune.ac.in> wrote: > Dear All, > > How to calculate structure factor and scattering intensity in gromacs

[gmx-users] Structure factor and scattering intensity in gromacs 5.1.4

Dear All, How to calculate structure factor and scattering intensity in gromacs 5.1.4. Thanks, Rakesh Sent with Mailtrack