[gmx-users] regarding charge group

The sum of the two largest charge group radii (13.336) is larger than rlist(1.2) - rvdw/rcoulomb i am getting this error while running membrane simulations. please any one suggest how to rectify this error. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Regarding membrane(DMPC) simulations with fullerene

Dear Sir, I am doing fullerene interaction with DMPC , i downloaded the gro file from the website mentioned in the tutorial. I was keep the fullerene on the top of DMPC. But in the gro file already water is present. If i removed that water molecules and adding new water

[gmx-users] membrane simulations

I am doing simulation of metal clusters with membranes by position restrain (with f=1000) the membrane. In this simulation the structure of metal cluster is collapsed after entering into membrane. I want to preserves its structure with out doing position restrain the metal cluster because it has

[gmx-users] freez gropus

I am doing simulation of metal clusters with membranes by position restrain (with f=1000) the membrane. In this simulation the structure of metal cluster is collapsed after entering into membrane. I want to preserves its structure with out doing position restrain the metal cluster because it has

[gmx-users] Dear Sir

Fatal error: [ file spc.itp, line 32 ] Atom index (1) in bonds out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. in that case move the settles section to the right molecule the above error i

[gmx-users] (no subject)

Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] pulling simulations

Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] metadynamics

Sir, i want to learn about metadynamics, how to run metadynamics in gromacs.please suggest me in this regard. Thank you. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] puuling simulations

Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. Thank You -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

[gmx-users] Fwd: puuling simulations

Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. Thank You -- regards M.SathishKumar -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] pulling simulations

Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. Thank You -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

[gmx-users] (no subject)

Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials for calculating youngs modules ,stress and strain. Thank You -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] (no subject)

hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

[gmx-users] (no subject)

I want to do simulation of protein at pH 12, in this case experimentally reported that the disulphide bonds of protein was broken and sulphurs become S negative . Can you please tell me making of disulphide as S- and S- is it correct and how to set force field to this.

Re: [gmx-users] Thiolate cysteine

Thank you sir On Mon, May 6, 2013 at 4:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/6/13 7:03 AM, Sathish Kumar wrote: I want to do simulation of protein at pH 12, in this case experimentally reported that the disulphide bonds of protein was broken and sulphurs become S negative

Re: [gmx-users] Reax force field

Thank you sir On Mon, May 6, 2013 at 4:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/6/13 6:51 AM, Sathish Kumar wrote: hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein

[gmx-users] (no subject)

I want to do simulation of protein at pH 12 so i have to deprotanate tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx command -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the

[gmx-users] (no subject)

Hai I have done 10ns simulation for a protein to this i want to calculate DCCM map.can you please suggest me how to calculate this map. Thank You. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

Re: [gmx-users] Re: Aspartate at high pH

Hai, I need to do simulation of protein at pH 12.I am unable to do that can you please tell me how to do and how to set up pH conditions. Thank You. On Wed, Feb 13, 2013 at 6:08 PM, Valentina valentina.erast...@durham.ac.ukwrote: Thank you Tsjerk! --

[gmx-users] Fwd: REgarding for the disulphide bond

-- Forwarded message -- From: Sathish Kumar sathishk...@gmail.com Date: Sun, Jan 27, 2013 at 2:02 PM Subject: REgarding for the disulphide bond To: gmx-users@gromacs.org Sir, I am sathish kumar working as junior research fellow.I have taken pdb file from protein data