[gmx-users] topology for oxygen molecule

Respectable Justin/Mark For the study of diffusion of oxygen in water, I tried to search the itp file for oxygen molecule but could not find. Therefore, I have tried to make it myself.   Please tell me whether it is fine.   [ moleculetype ] ; molname nrexcl OMOL 1 ; as there are two atoms in an o

[gmx-users] oxygen itp

Respectable Experts I am very grateful to Justin. Yes I have defined the atom OB with its mass in the ffgmx.atp file. I have also defined the residue OMOL in ffgmx.rtp file that I am using.   Thank you         ___ gmx-users mailing listgmx-us

[gmx-users] ffgmx:diffusion of oxygen

Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which matches with that given in the gromacs manual. After equilibrating my system of 1 oxygen and 255 water molecules in

[gmx-users] ffgmx:diffusion of oxygen

Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such simulations for mostl

[gmx-users] Re:trestart

Respectable Justin/David/Mark and all other Experts Grettings I am not clear about the function of the option -trestart in g_msd With trestart =0 the msd curve is very kinky which really improves to a smooth one when trestart=1 is set. But when I increase the value to 10, 20 and 100 ps the smoo

[gmx-users] density

Respectable Experts Grettings I am studying diffusion of an oxygen molecule in 255 molecule of SPC water. I need to determine diffusion coefficient at temperature 298 K and 1 atm pressure. In order to do that using editconf I scaled the density of the system including oxygen to 1g/l. I checked t

[gmx-users] diffusion coefficient of oxygen molecule

Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want

[gmx-users] diffusion coefficient of oxygen

Respected Experts I need your help In my study of diffusion of a oxygen molecule in 255 molecules of water, I previously used SPC water model with ffgmx force field with cutoff L-J and Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for diffusion coefficient of oxyge

[gmx-users] oxydiffusion

Respected experts Thank you a lot for your valuable suggestions for my previous mail.   Taking your advice I used SPCE water model with ffg43a1 forcefield. I modified the non bonded parameters for oxygen-water interaction taking the parameters from CRC as a source in the nonbonded parameter file.

[gmx-users] oxydiff

In the previous mail I forgot to attach the msd curve. Would you please give a glance at this graph in relation to my previous mail ??    Thank you for your consideration Neal <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

[gmx-users] (no subject)

All gmx users   I am a very new fellow in gromacs   My structure contains 52 residues of a parallel helices with the separation of about 2 nm. I created a box with the editconf as editconf -bt dodecahedron -c     ___ gmx-users mailing listgm

[gmx-users] (no subject)

hello gmx users I am a new fellow in gromacs My structure contains 56 residues belonging to parallel helices separated by about 2 nm. I used editconf as: editconf- -bt dodecahedron -c and editconf -bt dodecahedron -d 6.5 -c   where 6.5nm I used as separation of unit cells   Now when I so

[gmx-users] diffusion of oxygen in water

RESPECTABLE EXPERTS   HAPPY NEW YEAR   I am a beginner in gromacs. I want to know if it is possible to study the diffusion of oxygen (as solute ) gas in water (solvent) with the current features of gromacs.   Does gromacs present the required forcefields? How can I make the corresponding pdb fi

[gmx-users] Thank you

Respectable Mark Thank you very much for your immediate response. I have added new atom type in the ffgmx.atp file and also modified ffgmx.itp, ffgmxnb.itp. After that the pdb2gmx worked. I used genbox to add water in the oxygen molecule system. For now I have taken only 2 oxygen molecules with

[gmx-users] genbox

Respectable Mark I am studying diffusion of oxygen in water. Can I specify the number of water molecules for a particular size of box. For example, I need to have 98 water molecules and 2 oxygen molecules in one solution. After that I need to increase the number of oxygen molecules and decrease

[gmx-users] segmentation fault

Respectable Mark/David/Berk   I want to study diffusion of oxygen in water at constant pressure of 1 bar. I thus coupled my system with berendsen with the reference pressureof 1 bar. But my production run gave a segmentation fault.   But when I don't couple, it doesn't. What should I do?   Your

[gmx-users] (no subject)

Respectable Mark/Berk/David I am trying to study diffusion of oxygen in water at a constant pressure of 1 bar. When I run the production run of 1 ns then I get an warning message as follows and the run terminates. Please try to figure out what might have been wrong.   Grid: 35 x 35 x 35 cells WA

[gmx-users] (no subject)

Respectable Mark/Berk/David I am trying to study diffusion of oxygen in water at a constant pressure of 1 bar. My system contains 2 oxygen molecules in 110 water molecules of the box size 1.5 nm I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run mdp file.   When I run the

[gmx-users] (no subject)

Respectable David/Justin/Mark/Berk In my study of diffusion of oxygen in water, I solved the segmentation fault problem as below 1. At first I ran for 16 ps beyond which segmentation fault occured in the previous run. I generated the .gro file of that run 2. I then ran for 100 ps using the .gro f