[gmx-users] problem regarding gmx trjconv

mol -ur compact This command(s) makes each chain (out of the 6) whole, but the chains do not come together. So the hexamer as a whole still remains broken. Is there a way to solve this problem? Thanks and Regards, Saumyak -- === *Saumyak Mukherjee* Senior Research Fellow

Re: [gmx-users] (no subject)

s or > send a mail to gmx-users-requ...@gromacs.org. > -- === *Saumyak Mukherjee* Senior Research Fellow Solid State and Structural Chemistry Unit Indian Institute of Science Bengaluru - 560012 === -- Gromacs Users mailing list * Ple

[gmx-users] Calculation of Static Structure Factor in GROMACS-5.0.7

Dear Users, I want calculate the static structure factor of water in GROMACS-5.0.7. Which module shall I use for that? In gmx rdf there is an output option "-hq". What is the meaning of this output? Any help is highly appreciated. Regards, Saumyak -- Gromacs Users mailing list * Please

[gmx-users] total energy of a protein

Dear All, Is there any way of obtaining the total energy of a protein from GROMACS (including bond stretch, angle bend, dihedral, Coulomb, LJ, Coulomb-14 and LJ-14) other than using gmx mdrun rerun? ‌ ​Regards, Saumyak​ -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] query about coul-SR

> > > On 2/22/2018 1:07 PM, Saumyak Mukherjee wrote: > >> Dear Users, >> >> In the output of gmx energy, coul-SR means short range Coulomb >> interactions. So if I have coul-SR for a protein, does it give the total >> self-interaction energy (Coulomb) o

[gmx-users] query about coul-SR

Dear Users, In the output of gmx energy, coul-SR means short range Coulomb interactions. So if I have coul-SR for a protein, does it give the total self-interaction energy (Coulomb) of the protein? Any help is much appreciated. Thanks & regards, *Saumyak Mukherjee* Senior Research Fe

Re: [gmx-users] nrexcl=3: ambiguous?

actions between atoms connected by adjacent bonds does not apply. The > requirement for particular kinds of 1-4 interactions are imposed by > construction of the force field. > > Mark > > On Mon, Feb 19, 2018 at 6:34 AM Saumyak Mukherjee < > mukherjee.saumya...@gmail.com&g

[gmx-users] nrexcl=3: ambiguous?

gives output for 1-4 interactions. How is this possible? Any help/suggestion is appreciated. Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow, Prof. Biman Bagchi's Lab, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India. -- Gr

[gmx-users] regarding calculation of intra-residue energy

, the average self-energy of the protein is coming as 8108 kT from my program. Is this value plausible? Any comment/suggestion is appreciated. Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow, Prof. Biman Bagchi's Lab, Solid State and Structural Chemistry Unit, Indian Institute of Sci

Re: [gmx-users] Fatal error in grompp

> > On 11/27/17 5:25 AM, Saumyak Mukherjee wrote: > >> Dear All, >> >> I want to calculate the interaction energy between water and protein >> backbone. However, in mdp file, when I am using >> >> energygrps = SOL backbone >> >> ​grompp is

[gmx-users] Fatal error in grompp

energy groups Can someone kindly point out my mistake?​ Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow, Prof. Biman Bagchi's Lab, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India.‌ -- Gromacs Users mailing list * Pl

[gmx-users] Fwd: Potential gradient in NVE simulation

fourierspacing = 0.16 rvdw-switch= 1.0 vdwtype= Shift tcoupl = no pcoupl = no pbc = xyz DispCorr = EnerPres gen_vel = no ​Can you kindly suggest what I might be doing wrong or what modifications are required in this script?​ -- Thanks & regards, *Saumyak Mukhe

[gmx-users] Pulling in opposite directions

ion will move in +Z direction, while the other in -Z direction? Any help/suggestion is most welcome. Thanks and regards, Saumyak -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute

Re: [gmx-users] calculation of energy of individual water molecules in gromacs

Thanks a lot for your comments. I am doing the calculations using a self-written FORTRAN code. On 31 May 2017 at 17:23, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/31/17 12:24 AM, Saumyak Mukherjee wrote: > >> Thanks Justin for the reply. >> >> Suppos

Re: [gmx-users] calculation of energy of individual water molecules in gromacs

energygrps. Is there any other way? On 31 May 2017 at 05:39, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/30/17 1:52 AM, Saumyak Mukherjee wrote: > >> Dear users, >> >> I need to calculate the energy of individual water molecules in a 1 nm >> shell aroun

[gmx-users] calculation of energy of individual water molecules in gromacs

? Thanks and regards, Saumyak -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob : 8017292426 Alternative e-mail : saumyakmukher...@gmail.com

Re: [gmx-users] Regarding centering the molecule/protein during Simulation

https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chem

Re: [gmx-users] genion command

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 visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-

Re: [gmx-users] Calculation of dielectric constant

10.1103/PhysRevE.92.032718> > > Best > > Philip > > — > > Philip Loche > Department of Physics > Freie Universität Berlin > Arnimallee 14, Room 0.3.30 > 14195 Berlin, Germany > > phone: +49 (0)30/838-55279 > > > On 11. May 2017, at 07:49, Saumyak M

[gmx-users] Calculation of dielectric constant

appreciated. Thanks and regards, Saumyak -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob : 8017292426 Alternative e-mail : saumyakmukher...@gmail.com

Re: [gmx-users] Calculation of volume of protein hydration layer

On 2 May 2017 at 10:33, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 01/05/17 18:44, Saumyak Mukherjee wrote: > >> Dear Users, >> >> Can anybody please tell me how to calculate the volume of protein >> hydration >> layer as a function

[gmx-users] Calculation of volume of protein hydration layer

If this calculation is possible in GROMACS, please guide me how to do it. Thanks in advance, Saumyak -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob

[gmx-users] Calculation of Cv

uot; terms or anything else? Thanks and regards, Saumyak -- ==== *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob : 8017292426 Alternative e-mail : sau

Re: [gmx-users] simulation of molecules in solid state

Thanks Justin. On 18 April 2017 at 17:49, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/17/17 3:32 PM, Saumyak Mukherjee wrote: > >> Dear Users, >> >> I have a .cif (Crystallography Information File) of a crystal of charged >> molecules a

[gmx-users] simulation of molecules in solid state

myak -- ==== *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob : 8017292426 Alternative e-mail : saumyakmukher...@gmail.com smukher...@sscu.iisc.erne

[gmx-users] Use of LINCS during production run

Dear users, Can you please inform me, which LINCS condition (h-bond, all bonds etc.) should be used during final production run to get the most realistic results? Thanks & regards, Saumyak -- ==== *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagc

[gmx-users] Calculation of configurational entropy

rom this I am getting just a single entropy value. How an I get the entropy as a function of time? Thanks in advance, Saumyak -- ==== *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Scie

Re: [gmx-users] Pdb2gmx

tps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute o

Re: [gmx-users] potential energy of a system

gt; > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > --

[gmx-users] potential energy of a system

Dear users, Which terms are included in the total potential energy of a system? Does it have COUL-SR and LJ-SR only, or does it also include the 1-4 terms? Thanks in advance. Regards, Saumyak -- *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's

Re: [gmx-users] calculation of self energy of protein

Dear Justin, Is there any way to get just the interaction energy between protein and water? In this case, the energy should not contain the self or inherent energy. Thanks & regards, Saumyak On 27 March 2017 at 11:27, Saumyak Mukherjee <mukherjee.saumya...@gmail.com> wrote: > T

Re: [gmx-users] calculation of self energy of protein

Thank you very much. On 27 March 2017 at 02:22, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/26/17 4:49 PM, Saumyak Mukherjee wrote: > >> Dear Justin, >> >> Thanks for the reply. >> >> I have tried that already. I stripped out the protein tra

Re: [gmx-users] calculation of self energy of protein

other. Does it mean that the solvent-protein interaction energies are also involved? Thanks and regards, Saumyak On 26 March 2017 at 19:51, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/26/17 10:06 AM, Saumyak Mukherjee wrote: > >> Yes, I need to calculate the i

Re: [gmx-users] calculation of self energy of protein

Yes, I need to calculate the inherent potential energy of the protein. On 26 March 2017 at 14:33, Souparno Adhikary <souparno...@gmail.com> wrote: > Do you mean the potential energy of the protein? > > On 26 Mar 2017 14:24, "Saumyak Mukherjee" <mukherjee.saumya...@gm

[gmx-users] calculation of self energy of protein

in the system, such as the hydration layer around protein? Thanks and regards, *Saumyak Mukherjee* Junior Research Fellow Prof. Biman Bagchi's Group Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore - 560012 Mob : 8017292426 Alternative

[gmx-users] Read from XTC file

the conversion and directly read the trajectory from .xtc file. Is it possible in FORTRAN 90? ​Thanking you, Regards, Saumyak Mukherjee​ -- 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