[gmx-users] Regarding Extracting Coordinates of Solvent in FCS alone

Dear All, I have situation rite now like, I have to take the Solute and Solvent Coordinates from First Coordination Shell / FCS + Second CS. Please give me some suggestion for doing the same. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91

[gmx-users] Regarding ngmx with double precision

Dear All, While installing Gromacs in double precision, I am not able to make ngmx run. Is it because of lack of X libraries. I want to run ngmx trajectory viewer. So I kindly request you to suggest me to make ngmx run. Thank you in Advance *With Regards, Ravi Kumar Venkatraman

[gmx-users] Regarding trajectory file

in advance *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

[gmx-users] Re: gmx-users Digest, Vol 93, Issue 72

Dear All, Could anybody tell me how to take the coordinates of the first and second solvation shell with solute from the snapshots of MDS run. Which molecular viewer will be good for it. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91

[gmx-users] Regarding Molecular Viewer

Dear All, Could anybody tell me how to take the coordinates of the first and second solvation shell with solute from the snapshots of MDS run. Which molecular viewer will be good for it. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA

[gmx-users] Regarding Benzene Simulation

- C5-C4-H4 7 1 6 2 1 ; 180.00 4.60240 2 ; H- C-C5-C1 I am showing only the problem creating part, that is the Dihedral and Improper Dihedrals. Please help me sort this problem out. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore

[gmx-users] Regarding Improper Dihedral

parameter for ethylacetate and how to calculate it. Thank you in Advance *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] QMMM Compilation

Dear All, Is it possible to compile Gaussian 09 Linux with gromacs 4.5.4. If at all please help me in this regard. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Regarding ngmx

*Dear All, After Installing gromacs, ngmx not seems to work and going through the blogs I understood that it because of some X libraries. Could anybody suggest how to install these libraries and make ngmx work. Thank you* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc

[gmx-users] Regarding KALP-15 Simulation

5.482 0.985 1DPPCN44 1.680 5.338 0.995 1DPPCC55 1.808 5.301 0.932 1DPPCC66 1.929 5.396 0.953 Thank you in Advance. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx

[gmx-users] Regarding Simulation of KALP-15 in DPPC

in this regard. * *Thank you* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

[gmx-users] Regarding Dimer calculations

Dear all, Could anybody suggest me how to do dimer calculation using gromacs or guide me to some paper or journal that describes the same. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users

[gmx-users] Regarding TIP4P structure

Dear all, Could anybody send me the link for getting the tip4p tip3p and tip5p single water structure in gro/pdb or in anyother format. Thank you. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users

[gmx-users] Regarding Shell Molecular Dynamics

Dear All, Is it not possible to minimize using cg with flexible constraints? Thank you In advance. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Regarding Table Extension

the same. Thank you* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Regarding Minimization

*Dear all,** * *I wanted to minimize the energy of a single molecule. How emtol and emsteps I have to put to get optimised single molecule structure.* * * *Thank you** * * * *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users

[gmx-users] Regarding Extension of the potential lookup tables

*Dear All, Could anybody tell me what is the purpose of Extension of the potential lookup tables beyond the cut-off. I have read somewhere that the sum the smallest diagnol of the box and rlist should be equal to table-extension. Please explain me the same.* *With Regards, Ravi Kumar

[gmx-users] Regarding Extension of the potential lookup tables beyond the cut-of

*Dear All, Ok, I don't remember the site. But please explain me about the purpose of table extension. Thank you * *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Energy Minimisation

* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't

[gmx-users] Regarding Gromacs Algorithms

*Dear All, Could anybody suggest me some books or notes or some materials which will help me to understand the way gromacs algorithms work i.e. how neighbor group search works e.t.c. I kindly request you to suggest me other than the gromacs manual.* *With Regards, Ravi Kumar

[gmx-users] Regarding MKTOP

this problem. Thank you in advance. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

[gmx-users] Regarding Density

using genbox_d command line?* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

[gmx-users] NVT Equilibration

*Dear All, But I scaled the solvent box according to the density using editconf_d command line. Then I carried out EM and NVT equilibration.* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users

[gmx-users] NVT equilibration of ethanol in OPLSAA ff

didn't use any shift or switch function. (can anybody suggest me a good tutorial to understand the judicious use of this functions.) Please help me sort this problem. If you need further details I am ready to send you. Thank you. With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, INDIA. -- gmx

[gmx-users] NVT equilibration.

mdrun_d -deffnm em I saw em.gro using VMD. Now I see ethanol molecules arranged all over thebox in order. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] NVT equilibration of Ethanol in OPLSAA.

in the box. I tried running at faster time scales like 0.2 fs then also I was getting the same. Please help me to overcome this problem. With regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] NVT Equilibration getting blown up

fs steps. cut-off length was 1.0 nm. Berendsen Thermostat at 298.15 k with 0.1 ps time constant. lincs constraint for all-bonds. Please suggest me something so that I can simulate without blowing up my system. Thank you, With Regards, Ravi Kumar Venkatraman. -- gmx-users mailing listgmx

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 166

be got from PRODRG server. Thank you. Yours Sincerely, Ravi Kumar Venkatraman, Ph.D., IPC Dept., IISc, INDIA. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

[gmx-users] Regarding OPLSAA

be got from PRODRG server. Thank you. Yours Sincerely, Ravi Kumar Venkatraman, Ph.D., IPC Dept., IISc, INDIA. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 167

Dear Justin, Thank you very much for your immediate reply and your help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

[gmx-users] regarding xtc file

-e *.edr -c *.gro -n *.ndx Is there anything wrong in the above commands or atleast why I am not able to view the trajectory using .trr file. Please suggest me something. Thank you. Ravi Kumar Venkatraman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] Regarding xtc

Dear Abraham, Thank you for your previous suggestion, I included nstxout, nsrvout and xtc_precision to output control. Now I am getting .xtc file but still it shows nothing in VMD but it read the frames while starting. Thank you. -- gmx-users mailing list

[gmx-users] regarding genbox

Dear all, I wanted to insert two different solute in a same solvent box. Can anybody suggest me how to do it. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Regarding mdrunfor small organic molecules

Dear All, When I try to grompp to generate .tpr file for mdrun from topology generated by prodrg I am getting the following error. Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'PRODRG'

[gmx-users] Re: Regarding mdrunfor small organic molecules

Dear all, Please can anybody send, step by step mdrun for small organic molecules in gromacs. Dear All, When I try to grompp to generate .tpr file for mdrun from topology generated by prodrg I am getting the following error. Generated 279 of the 1225 non-bonded

[gmx-users] Dear Lemkul

I could not find out what is wrong I tried add to add #include ions.itp and #ifdef but it is not successful. Fatal error: No such moleculetype SOL Please help me. I got stuck with this. Please. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Regarding parametrisation

Dear Justin, I was reading one of your literature on building GROMOS-compatible small molecule topologies. I was trying to reproduce the AM1BCC partial charges for the p-cresol using Antechamber from amber tools version 1.5. I will enlist what I have got and with literature

[gmx-users] Regarding Equilibration

Dear all, Could you please tell me what kind of error limit is accepted for running NVT and NPT equilibration in terms of Temperature, Pressure and Density. Thank you, With Regards, Ravi Kumar V IPC Dept., IISc, INDIA. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] How to run solvation dynamics for some organic molecules

Dear all, I have generated .gro and .top file for Chloranil from prodrg and tried solvate it using pre-equilibrated cyclohexane. When i tried to generate the box containing solute it is not modifying the .top file and it shows zero solvent. Please help me how to solvate organic

[gmx-users] Regarding Segmentation fault during mdrun_d

Dear All, I was trying to run NVT equilibration for cyclohexane. When I started running it shows following error Reading file nvt.tpr, VERSION 4.5.4 (double precision) Starting 2 threads Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'Cyclohexane box' 5 steps,100.0

[gmx-users] Regarding generating topology file.

to this. Thank you. *With Regards,** * * * *Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy,** * *IPC Dept., IISc.,* *Bangalore, INDIA.* *Phone No: +91-9686933963* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Regarding PDB file

0.38 17.96 O CONECT 48 981 CONECT 238 889 CONECT 513 630 CONECT 601 724 CONECT 630 513 CONECT 724 601 CONECT 889 238 CONECT 981 48 Is this right or I have to delete some other things also. Thank you *With Regards,** * * * *Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy

[gmx-users] Running Lyz in water

6091 solvent instead of 10832 as per tutorial. Pls help me find the problem. Thank you *With Regards,** * * * *Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy,** * *IPC Dept., IISc.,* *Bangalore, INDIA.* *Phone No: +91-9686933963* -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Re: Running Lyz in water

but it shows fatal I/O error - topol.top. It was not able to find the input file topol.top. But in this tutorial its an output command. Further it shows 6091 solvent instead of 10832 as per tutorial. Pls help me find the problem. Thank you *With Regards,** * * * *Ravi Kumar Venkatraman

[gmx-users] Regarding NPT Eq.

Dear All, I have been trying to do NPT equilibration for 100 ps. I have tried with different tau_p like from 0.5 to 2 and my reference pressure is 1 bar. Since I am continuing from 20 ps NVT equilibrated configuration, in npt.mdp I have written init_step = 1 (1*0.02 fs = 20 ps). But

[gmx-users] How to simulate spc216.pdb in different water potentials

in advance *With Regards,** * * * *Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy,** * *IPC Dept., IISc.,* *Bangalore, INDIA.* *Phone No: +91-9686933963* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] (no subject)

Dear Sir/Madam, In gromacs tutor we have water .gro file for spc potential. How to get .gro files from spc216.pdb of different potentials like tip3p tip4p ... etc. -- With Regards, Ravi Kumar Venkatraman, c/o Prof. Siva Umapathy, IPC Dept., IISc., Bangalore, INDIA. Phone No: +91