Re: [gmx-users] Finding the distribution of counterions around the polymer (polyelectrolyte) at larger scales

Dear all, I have used the radial distribution functions to examine the structure and distribution of ions in the proximity of the polyelectrolyte and studied the spation distribution of ions at the smallest length scales. I have to now examine the distribution of counterions at larger scale as

Re: [gmx-users] output file format under pbc

Dear Users, It works with the following command. > trjconv -f confout.gro -o output.gro -pbc whole Thank you. Best regards, Changwoon Jang On Fri, Aug 26, 2016 at 9:21 AM, Marlon Sidore wrote: > Hello, > > If you want your molecule whole, the -pbc mol option of

[gmx-users] GB parameter(s) missing or negative for atom type 'xxx'.

Hi, I want to simulate a protein-ligand complex with implicit solvent. After I ran "grompp" command it prompted me there were some missing GB parameters. I guess the problem is that some atom types in my system are not included in the gbsa.itp file. If it is the case, do you know where can I find

Re: [gmx-users] How to calculate radial distribution functions ...(Justin Lemkul)

Dear Justin, Thanks for your reply. I gave a command a O r1 and O atoms from residue 1 were selected as O_r1. Thanking you, yours sincerely, Apramita -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] How to calculate radial distribution functions when atoms in different amino acids are named similarly

On 8/26/16 9:37 AM, Apramita Chand wrote: Dear All, Following is a portion of my .top file showing the naming of atoms of two of my amino acids of my protein residue 22 TYR rtp TYR q +1.0 1 NL 22TYR N 1 0.12914.0067 ; qtot 0.129 2 H

[gmx-users] How to calculate radial distribution functions when atoms in different amino acids are named similarly

Dear All, Following is a portion of my .top file showing the naming of atoms of two of my amino acids of my protein residue 22 TYR rtp TYR q +1.0 1 NL 22TYR N 1 0.12914.0067 ; qtot 0.129 2 H 22TYR H1 1 0.248

Re: [gmx-users] output file format under pbc

Hello, If you want your molecule whole, the -pbc mol option of trjconv is probably what you're searching for. Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-08-26 15:05

[gmx-users] Regarding correct way to calculate diffusion constant

Dear All, I want to calculate the diffusion constant of urea in my system. I used g_msd for this purpose and the value came to be 8.279e -08 (+/-8.85e-09) 1e -5 cm^2/s. Since the value is quite low, I wanted it to check it with result from VACF. So I used the commands: g_velacc -acflen 1001 -no

Re: [gmx-users] output file format under pbc

Dear Justin Lemkul, Thank you. I am going to try it. I tried to understand trjconv via the manual. Best regards, Changwoon Jang -- 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

Re: [gmx-users] output file format under pbc

On 8/25/16 11:36 PM, Chang Woon Jang wrote: Dear Gromacs Users, I would like to describe the situation. An initial molecule in the periodic boundary condition is located near the right side of box. The box is big, thus needs to be adjusted and equilibrated under NPT. The box should be

[gmx-users] X Amino Acids for Building CG Structure

Hi, I just got "X" amino acids on DSSP, what does it means ? when I use the DSSP file to build coarse grained structure with martini 2.2 force field, I lost some amino acids because of this "x" amino acids on DSSP. So, how to build CG structure if I have this "x" amino acids ? I want to build CG