[gmx-users] question on ffG43a1p force field

Sorry for this basic question. I read previous emails and tried to make pdb2gmx find ffG43a1p.ff. I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also tried to create a file called forcefield.doc and wrote "ffG43a1p" into it. I put these files in working directory and /usr/local/gr

Re: [gmx-users] Regarding too many LINCS warnings for bicarbonate ion

Den 2019-08-16 kl. 06:45, skrev Apramita Chand: Dear Gromacs users, I am trying to use bicarbonate ions in my simulations employing AMBER99SBILDN ff in GROMACS 5.1.4. For that I've used the antechamber and acpype utilities to generate the parameters for Bicarbonate with RESP charges at HF/6-31G*

[gmx-users] Regarding too many LINCS warnings for bicarbonate ion

Dear Gromacs users, I am trying to use bicarbonate ions in my simulations employing AMBER99SBILDN ff in GROMACS 5.1.4. For that I've used the antechamber and acpype utilities to generate the parameters for Bicarbonate with RESP charges at HF/6-31G* level of theory. No matter how many times I change

Re: [gmx-users] How to create a group for a set of atoms with make_ndx

Hi.. The command is given below gmx make_ndx -f *.gro -o *.ndx You need to see inside the gro file what are the residue index corresponding to the particular residue Next...When atom selection will appear you select the residues like r66|r65|...So on upto the last residue...And you can name the gro

Re: [gmx-users] Gromacs-GPU help

Hi, You may wish to search the list archives as indicated at: Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! See also: https://arxiv.org/abs/1903.05918 Benson On 8/16/19 5:37 AM, tarzan p wrote: Hi all,I have started using GROMACS r

[gmx-users] Gromacs-GPU help

Hi all,I have started using GROMACS recently on my work station (2 X Intel 6148 (20 cores each) and 2 x tesla v100 .I have compiled it as per the instructions atRun GROMACS 3X Faster on NVIDIA GPUs | | | | | | | | | | | Run GROMACS 3X Faster on NVIDIA GPUs Complete your molecular dy

Re: [gmx-users] Difference between residue (r) and residue index (ri) when selecting residue groups?

On 8/15/19 12:16 PM, Dhaniram Mahato wrote: r will select all atoms without hydrogens. ri will select all atoms including all hydrogens too. This is not correct. GROMACS has default groups with and without hydrogens. r selects based on the actual residue number. ri is supposed to select ba

Re: [gmx-users] How to create a group for a set of atoms with make_ndx

Index file is always in a serial no. You can check the residue serial no. by opening the pdb in text format. "gmx make_ndx " is the command to use to see all indices and then choose your residues accordingly. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Su

Re: [gmx-users] Difference between residue (r) and residue index (ri) when selecting residue groups?

r will select all atoms without hydrogens. ri will select all atoms including all hydrogens too. -- 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_Lis

Re: [gmx-users] Running on two nodes

Or May be you can keep the options as default. Then mdrun will automatically use all the resources available. -- 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/Suppor

Re: [gmx-users] inter-residue contact map

Hi Shahee, If you are willing to go beyond GROMACS you could also do this with Biopython (see for example https://github.com/biopython/biopython/issues/2163) or BioJulia (see https://biojulia.net/BioStructures.jl/stable/documentation.html#Spatial-calculations-1). Best, Joe On 15/08/2019 11:0