[gmx-users] electrostatic and LJ energy

You can use gmx energy (g_energy). Follow the online manual at http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-energy.html Regards -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] doubt regarding order parameter calculated by gmx chi S2max and S2min

Dear Mario, You can calculate NH order parameter (or any other bond order parameter) by following method https://extras.csc.fi/chem/courses/gmx2007/analysis/ However I was curious about gmx chi which was supposed to give dihedral order parameter. -- Gromacs Users mailing list * Please search

[gmx-users] doubt regarding order parameter calculated by gmx chi S2max and S2min

Hi Everyone, Is the S2max and S2min produced by gmx chi is same as Ss (slow order parameter)and Sf (fast order parameter) respectively. If not may anybody please explain what are those (S2max and S2min). Thanks a lot. Sincerely Tushar -- Gromacs Users mailing list * Please search the archive

[gmx-users] download GROMOS54a6oxy

Hi all, I wish to use GROMOS54a6oxy forcefield parameterized by Horta et. al. However, I am unable to find any link to download the same. It will be a great help if any one send me the link or the forcefield. Thanks a lot. Tushar -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Assigning charge to closely related functional group

to assign correct partial charges. Thanks a lot for the help. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

[gmx-users] Mentioning LJ Cutoff in mdp file

Hi Everyone, I want to use LJ interaction cutoff at 12 Å and treat LJ smoothly between 10 and 12 Å. Does the following in .mdp file reflect the same? rvdw-switch = 0.2 rvdw = 1 Kindly Reply. Thanks a lot. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student

Re: [gmx-users] How to obtain TIP4P/? water model topology file

Hi Mark, Thanks a lot for the suggestion. I will try it. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

Re: [gmx-users] How to obtain TIP4P/ε water model topology file

deg) * 0.09572 nm] ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) [ virtual_sites3 ] ; Vsite fromfunctab 412310.128012065 0.128012065 Thanks a lot. On Wed, Feb 21, 2018 at 10:48 AM, Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote:

Re: [gmx-users] How to obtain TIP4P/ε water model topology file

parameters are mentioned). I have experimental data to verify if the water model is not appropriate. It will be a great help if you can help me getting/creating the topology. Thanks a lot for your suggestion. On Tue, Feb 20, 2018 at 10:00 PM, Tushar Ranjan Moharana < tusharranjanmohar...@gmail.

[gmx-users] How to obtain TIP4P/ε water model topology file

Hi All, I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone let me know where can I get the corresponding .itp file. Thanks a lot. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Stu

Re: [gmx-users] Regarding calculation of Lennard-Jones potential

You can do that by g_energy (or gmx energy). but before that you have to create separate energy group and mention in .mdp file prior to md run. or you can rerun the trajectory with above changes. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list

[gmx-users] unsatisfactory result for kinetic energy using trj ekt and ekr

also let me know. Thanks a lot. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-

Re: [gmx-users] convert .tpr to include energy groups

Thanks a lot Justin. On Wed, Aug 9, 2017 at 1:33 AM, Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi All, > I want to calculate interaction between 2 energy groups, which were not > defined during the run. So I want to rerun and include both the energy

[gmx-users] convert .tpr to include energy groups

and by mistake the .gro and .cpt file got overridden. Kindly suggest if there is any way to achieve the above things. Thanks a lot. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gro

Re: [gmx-users] protein protein interaction: side chain contribution

Hi Justin, Thanks a lot for the valuable advice. "A society with free knowledge is better than a society with free food" On Fri, Jul 7, 2017 at 3:04 PM, Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi Justin, > Thanks a lot for the advice. It lo

Re: [gmx-users] protein protein interaction: side chain contribution

time and effort. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befo

[gmx-users] protein protein interaction: side chain contribution

time and efforts. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befo

[gmx-users] Doubt regarding enthalpy calculation

environment? Kindly help me understand the above. Thanks a lot "A society with free knowledge is better than a society with free food" -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.g

[gmx-users] Adding a new(modefied) fatty acid to charm 36 force field.

0.14510 306165.0 1 10 1 0.10930 287014.9 0.10930 287014.9 -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

[gmx-users] doubt regarding mdp option for rerun

for nsteps, if I want to rerun only the second xtc. 2) Can I combine them to get a continuous xtc file. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Calculating change in folding free energy due to mutation

and the mutant. Here is a paper where Seifollah *et al*. have done a similar work. The work I want to do is simpler as it doesn't involve membrane. http://www.ncbi.nlm.nih.gov/pubmed/25427619 Thanks a lot. "A society with free knowledge is better than a society with free food" Tushar Ranja

[gmx-users] calculate change in delta G of folding due to mutation

. Thanks a lot. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] doubt about "Ignoring obsolete mdp entry"

"A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] Preparing dual topology for free energy calculation

( map(lambda a: a.name, atoms1)),'-'.join( map(lambda a: a.name, atoms2)) ) Thanks a lot. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archi

[gmx-users] Preparing dual topology for free energy calculation

t; Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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_Lists * For (un)subscribe requests v

Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

Hi SAKO MIRZAIE, Thanks for your reply. But how can we calculate difference in folding free energy by doing 2 separate simulations? Please clarify (at least give some hints or references). Thanks a lot. "A society with free knowledge is better than a society with free food" -- Tus

[gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

way (like pdb2gmx or any other program). If not then can any body explain me the way to do so(I can write perl script if necessary). Thanks a lot for your time and effort. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Waranga

[gmx-users] potential energy between 2 energy group

for your valuable advice. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_L

[gmx-users] Calculate energy associated with hydrogen bond

ledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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.o

[gmx-users] Query regarding energy calculation

extracted by gmx energy (g_energy). Thanks a lot for the help. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

Re: [gmx-users] Installation of two versions of Gromacs on one system

Hi Peter, Try this whenever opening a new terminal source /path/to/gromacs/bin/GMXRC What ever version you want to use mention corresponding path. "A society with free knowledge is better than a society with free food" Best Regards Tushar Ranjan Moharana B. Tech, NIT Warangal Ph

Re: [gmx-users] Calculate NMR shift from simulation

Hi Andrea, Thanks for your precious advice. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

[gmx-users] Calculate NMR shift from simulation

number of solvent molecule within 0.4 nm. However nothing correlated with observed shift (correlation coefficient less than 0.02). Any advice is precious and I am thankful for the same. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B.

[gmx-users] Explicit and implicit solvent

Hi everyone, I am really confused between explicit and implicit solvent model. Any good resource will be helpful to me. I am using CHARMM forcefield and TIP4P water model. I guess it is explicit water model. Can anyone correct me? Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB

[gmx-users] Does .xtc enough for all kind of analysis?

ciety with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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.g

[gmx-users] Analyze neighbors of a residue within a cutoff distance during simulation

succeed. Can anybody kindly suggest me which analysis tool will be useful for me. Thanks a lot in advance. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Ple

Re: [gmx-users] Probable bug in 5.0.4 gmx enemat

/s/y9ia804dh0766pe/energy_groups.dat?dl=0 Thanks alot for your time and consideration. A society with free knowledge is better than a society with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] calculate average and maximum non-bonded energy between energy groups

knowledge is better than a society with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

Re: [gmx-users] calculate average and maximum non-bonded energy between energy groups

with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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_Lists * For (un)subscribe

[gmx-users] calculate avarage and maximum non-bonded energy between energy groups

framesSegmentation fault (core dumped)* I tried 4.6.7 version and install GROMACS in debug mode but nothing worked for me. Can anybody suggest me something. Little hint will also be helpful. Thanks a lot in advance. A society with free knowledge is better than a society with free food Tushar Ranjan

Re: [gmx-users] Probable bug in 5.0.4 gmx enemat

. A society with free knowledge is better than a society with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

Re: [gmx-users] How to mention torsional parameter in toplogy

knowledge is better than a society with free food Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

[gmx-users] Segmentation fault (core dumped) during EM

and effort. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB A society with free knowledge is better place to live than a society with free food. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Pi stacking

field and water model one should use for simulating a system (preferably protein in water) at different salt concentration to see the effect of salt concentration on the structure of the protein. Thanks a lot for your time and advice. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student

Re: [gmx-users] Pi stacking

using GROMACS please let me know how. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

Re: [gmx-users] Topology error

PRODRG generate topology for GROMOS force field (united atom) that's too with wrong charge. GROMOS force field doesn't consider non polar hydrogen. If you want to use GROMOS force field, then just go ahead without counting hydrogen. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB

Re: [gmx-users] periodic boundary conditions pbc=xyz

Hi Ming Use *-pbc mol* while using trjconv. Anyway it is not another box. Best Regards -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB, INDIA -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] System size increases and exceeds unit cell dimensions during simulation.

conditions: xyz, no, xy pbc = xyz periodic-molecules = no Any suggestion is most welcome. Thanks for your valuable time and suggestion. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Error while using pbc = xy Segmentation fault (core dumped)

subsequent line. Please help me in solving the problem. Thanks a lot. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

[gmx-users] (no subject)

in solving the problem. Thanks a lot. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

Re: [gmx-users] Problem in making index.ndx and disres.itp

loup1up2 weight So what do you suggest me to do? Thanks in advance. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] problem in defining protonation state of amino acids

Hi Justin, Thanks for your valuable suggestion. I ignored the hydrogen and added manually bu -his flag. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Problem in making index.ndx and disres.itp

0.025981 0.2259811.22598 1 1012 164 1 0.0259023 0.225902 1.2259 1 1112 165 1 0.122624 0.3226241.32262 1* -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please

[gmx-users] problem in defining protonation state of amino acids

sorting atoms. I can remove the error by adding -ignh but my concerned is this may change the protonation state. Please help me with your valuable suggestion. Thanks for your time and effort. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please

Re: [gmx-users] Unable to maintain proper density of polyunsaturated fatty acid

Hi Justin, Thanks for your valuable suggestion. Now my problem got solved. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

[gmx-users] Unable to maintain proper density of polyunsaturated fatty acid

after energy minimization was positive (order of 10^2) in this case too. Any suggestion to try is most welcome. Thanks for your time and effort. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] (no subject)

modification I shall do to any file of that forcefield. Any help or advice will be precious to me Thanks for your time and effort -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists