[gmx-users] Buckingham parameters to Lennard Jones Parameters

Hello Group, Can anyone please tell me as how can i convert Buckingham potential parameters into Lennard Jones parameters? Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Using different sets of parameters with the same functional form for a single dihedral

Hello Group, I want to define dihedral potential for a particular dihedral in GROMACS. My problem is that i have eight sets of parameters with *different multiplicity (n)* and f*orce constant value (k)* for the same dihedral of *functional form 1*.

[gmx-users] Doubt regarding gmx msd

Dear gmx users, I want to calculate mean square displacement (MSD) for three chains in my system. And for this i have prepared separate index file for all the three chains in my system. And i am running the gmx msd command using these index file. But i am confused as how i can

[gmx-users] How to post a reply on user list?

Respected Sir, I wanted to know that after posting a question on the list and getting a answer for that, from where i can post a reply on the user list if i want to discuss some more issues related to that particular question. I know that the question is silly but i am

[gmx-users] Criteria used to get DIHEDRAL DISTRIBUTION at discrete points

Hello List, I wanted to know that when we calculate dihedral distribution in GROMACS using gmx angle, it gives us values at discrete points like -180,-179 etc then what happens to the angles that falls in between -180 and -179? And what criteria is used to decide that a value lying in

[gmx-users] Easiest way to calculate the POTENTIAL ENERGY of a single isolated chain in GROMACS

Hello list, Can anyone please tell me about how can i calculate the POTENTIAL ENERGY of a single isolated chain in the most easiest way in GROMACS. Cheers, SK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] How to use LENNARD JONES 9-6 potential form in GROMACS

Hello List, Can anyone tell me regarding how can i use Lennard Jones 9-6 potential form in GROMACS. Thanks, SK -- 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

[gmx-users] How to decide the PRESSURE COUPLING CONSTANT VALUES and TEMPERATURE COUPLING CONSTANT VALUES

Hello list, I am preparing an amorphous sample using GROMACS but i am not able to get the required density of the amorphous polymer. I am having reasonable force field parameters and compressibility factors values. So i am thinking that there must be some error with the coupling constant

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 166, Issue 49

-- Performing Test CXX11_STDLIB_PRESENT > >>>> -- Performing Test CXX11_STDLIB_PRESENT - Failed > >>>> CMake Error at cmake/gmxTestCXX11.cmake:210 (message): > >>>> This version of GROMACS requires C++11-compatible standard > library. > >

[gmx-users] Do i need to put POSITION RESTRAINT DURING EQUILIBRATION STAGE ( NVT ) if i am preparing an amorphous sample?

Thank you Krzysztof Makuch for your valuable suggestion. Regards SK -- 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] Do i need to put POSITION RESTRAINT DURING EQUILIBRATION STAGE ( NVT ) if i am preparing an amorphous sample?

Hi list, I am preparing an amorphous sample using GROMACS but i am in doubt that during the equilibration stage ( NVT & NPT ) do i need to put position restraint on my polymer as there are no solvent in my system and if i have to use position restraint then why i should do that? THANKS, SK --

[gmx-users] Finding out the RDF between the COM of all the residues present in Group 1 with the COM of all the residues present in Group 2

Dear all, Can anyone please tell me the proper command in GROMACS to calculate the RDF between the COM of all the residues present in Group 1 with the COM of all the residues present in Group 2. Thanks & Regards, Sanjeet -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Running no periodic boundary condition simulation in GROMACS

Dear all, I want to run no pbc simulation for a single chain in GROMACS inorder to find out the forcefield applied potential energy of the chain. Can anyone please tell me how to do it? Thanks in advance -- Gromacs Users mailing list * Please search the archive at