Re: [gmx-users] Hydrogen existence time

Emanuel, Am trying out the procedure u have mentioned but on the other hand i found out a article which mentions does the same. https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html The article states- use the g_hbond program to analyse hydrogen bonds. First select protein twice, to

[gmx-users] Hamiltonian REMD code uploaded in gromacs / user contributions / other software

Assist Prof. Yuguang Mu School of Biological Sciences Nanyang Technological University 60 Nanyang Drive, Singapore 637551 Office: 04s-46 Tel: +65-63162885 Fax: +65-67913856 Email:y...@ntu.edu.sg CONFIDENTIALITY: This email is intended solely for the person(s) nam

[gmx-users] reg g_sas

Dear justin ,     Thank you for your previous reply.        I would like to get only one value of solvent Accessible area which may be average of all time frames instead of .xvg files can i get it. Also can i correlate pullf.xv

Re: [gmx-users] reg g_sas

vidhya sankar wrote: Dear justin , Thank you for your previous reply. I would like to get only one value of solvent Accessible area which may be average of all time frames instead of .xvg files can i get it. Av

[gmx-users] postdoc positions in chemical physics

Hi all, Just to inform you about the new openings in our team. = August 2011 POSTDOCTORAL SCHOLAR POSITIONS THEORETICAL AND COMPUTATIONAL CHEMICAL PHYSICS Postdoctoral positions are immediately available in the theory group of Professor Oleg Prezhdo.

[gmx-users] To Justin

Dear justin,   i am extremely sorry for  inconvenience  Thank you -- 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 pos

Re: [gmx-users] To Justin

vidhya sankar wrote: Dear justin, i am extremely sorry for inconvenience If I were inconvenienced, I never would have replied at all. I just want to make it very clear that there's no way for anyone to give you help remotely about a system they know no

[gmx-users] LJ-14 / LJ(SR)

Hello everyone, I know the following question has been discussed many times in the archive but unfortunately I am still unclear about it therefore I would like to ask for your patience. I am interested in non bonded interactions, i.e LJ(SR) and it has been said that LJ-14 potentials are *inter*mo

Re: [gmx-users] LJ-14 / LJ(SR)

Juliette N. wrote: Hello everyone, I know the following question has been discussed many times in the archive but unfortunately I am still unclear about it therefore I would like to ask for your patience. I am interested in non bonded interactions, i.e LJ(SR) and it has been said that LJ-

Re: [gmx-users] LJ-14 / LJ(SR)

On 26 August 2011 12:06, Justin A. Lemkul wrote: > > > Juliette N. wrote: > >> Hello everyone, >> >> I know the following question has been discussed many times in the archive >> but unfortunately I am still unclear about it therefore I would like to ask >> for your patience. >> >> I am intereste

[gmx-users] Error from residues added to rtp file

Dear Gromacs users, I am currently trying to run an MD simulation with the OPLS-AA force field on a protein having different non standard residues and a ligand. I found the charges for the OPLS force field for these residues in the literature and I am now trying to add them in the OPLS force f

Re: [gmx-users] Error from residues added to rtp file

Hi, I think the problem is that you have a dash rather than a minus symbol for the sign of the charge on the OD atom. Cheers Tom Delmotte, Antoine wrote: Dear Gromacs users, I am currently trying to run an MD simulation with the OPLS-AA force field on a protein having different non standa

Re: [gmx-users] Error from residues added to rtp file

Oh, thank you so much! That was indeed the error. It's amazing how these little things can sometimes drive you mad Thanks a lot, Antoine On 08/26/2011 05:27 PM, Thomas Piggot wrote: Hi, I think the problem is that you have a dash rather than a minus symbol for the sign of the charge on

[gmx-users] coordinated of center of mass

Hi all: I have a multiconponent system and for each component I wish to know the center of mass (COM) coordinates. I know that g_dist can give me the distances between the center of masses, but I do not want only the distances, I and interested in the x y and z coordinates as well. Could anyo

[gmx-users] Re: LJ

>> >>> Hello everyone, >>> >>> I know the following question has been discussed many times in the archive >>> but unfortunately I am still unclear about it therefore I would like to ask >>> for your patience. >>> >>> I am interested in non bonded interactions, i.e LJ(SR) and it has been >>> said th

[gmx-users] Re: LJ

>>. Now it is clear that >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. Thank >> you so much. The answer actually depends on what you call "nonbonded potential". If you want to calculate e.g. the interaction energy between two molecules, then you should NOT include this t

Re: [gmx-users] coordinated of center of mass

Hi Shikha, Have a look at g_traj -ox -com Cheers, Tsjerk On Aug 26, 2011 6:46 PM, "shikha nangia" wrote: Hi all: I have a multiconponent system and for each component I wish to know the center of mass (COM) coordinates. I know that g_dist can give me the distances between the center of masse

Re: [gmx-users] Re: LJ

On 26 August 2011 13:25, Dr. Vitaly V. Chaban wrote: > >>. Now it is clear that > >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. > Thank > >> you so much. > > The answer actually depends on what you call "nonbonded potential". If > you want to calculate e.g. the interact

Re: [gmx-users] Re: LJ

Juliette N. wrote: On 26 August 2011 13:25, Dr. Vitaly V. Chaban > wrote: >>. Now it is clear that >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. Thank >> you so much. The answer actually depends on what you call "

Re: [gmx-users] Re: LJ

On 26 August 2011 15:17, Justin A. Lemkul wrote: > > > Juliette N. wrote: > > >> >> On 26 August 2011 13:25, Dr. Vitaly V. Chaban > vvcha...@gmail.com>> wrote: >> >> >>. Now it is clear that >> >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded >>potentials. Thank >> >>

Re: [gmx-users] Re: LJ

Hi Juliette, Formally, you can kill this energy by going to the main topology file (like ffgmx.itp) and setting FudgeLJ term to zero, although I think that you don't actually want to do so. LJ-14 is the energy between the atoms belonging to the SAME molecule, so if you consider e.g. heat of vapori

Re: [gmx-users] Re: LJ

Dr. Vitaly V. Chaban wrote: Hi Juliette, Formally, you can kill this energy by going to the main topology file (like ffgmx.itp) and setting FudgeLJ term to zero, although I think that you don't actually want to do so. LJ-14 is the energy between the atoms belonging to the SAME molecule, so if

Re: [gmx-users] Re: LJ

>Thank you so much for your explanation. I am just guessing in the last >statement you meant *inter* molecular! Yes. INTERmolecular, between chemically nonbonded particles. >> >> Formally, you can kill this energy by going to the main topology file >> (like ffgmx.itp) and setting FudgeLJ term to

[gmx-users] If the system net charge is zero, do I need to add ions?

Hi GROMACS users, I've two questions. My simulation box contains a DMPC lipid bilayer, water molecules, intramembrane protein and a ligand protein. The net charge of the system is zero. Is it necessary to add ions to this system? The intramembrane protein (made of two chains) has a net charge

Re: [gmx-users] If the system net charge is zero, do I need to add ions?

Dr. Ramón Garduño-Juárez wrote: Hi GROMACS users, I've two questions. My simulation box contains a DMPC lipid bilayer, water molecules, intramembrane protein and a ligand protein. The net charge of the system is zero. Is it necessary to add ions to this system? A net neutral system can b