[gmx-users] Reg: REMD result

't understand the result according to this output it seems no exchange has taken place. What should be the output if an exchange has occurred. Thanks Rohit -- Rohit Farmer PhD Biosciences (2011-2014) Center for Systems Biology University of Birmingham Birmingham B152TT United Kingdom Email : r

[gmx-users] Reg: REMD error

Hi there, I am running the REMD and I got the following error Fatal error: The properties of the 8 systems are all the same, there is nothing to exchange can anyone explain me what it is about and what should i do to solve it. Thanks Rohit -- Rohit Farmer PhD Biosciences (2011-2014

[gmx-users] Reg: Number of nodes in REMD

is also not working. I installed gromacs_mpich using synaptics in ubuntu. Any help please. Thanks Rohit -- Rohit Farmer PhD Biosciences (2011-2014) Center for Systems Biology University of Birmingham Birmingham B152TT United Kingdom Email : rohit.far...@gmail.com -- gmx-users mailing list

[gmx-users] Re: gmx-users Digest, Vol 93, Issue 54

Concatenating RMSD plots (Rohit Farmer) 2. Re: Fw: [gmx-users] trjconv in martini (mohammad agha) 3. Re: Coupling groups - Thermostat (Justin A. Lemkul) 4. Re: Concatenating RMSD plots (Justin A. Lemkul) 5. Re: Coupling groups - T

[gmx-users] Concatenating RMSD plots

Hi there, I have just run several simulations of my system using different seeds and now i want to plot the RMSDs for different seeds in one plot for comparison. Is there any way to do it. Thanks Rohit -- Rohit Farmer PhD Biosciences (2011-2014) Center for Systems Biology University of

[gmx-users] Reg: Langevine Thermostat

Hi guys ... Happy New Year Does anyone know how to use Langevine Thermostat in gromacs. Thanks Rohit -- 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 p

[gmx-users] Reg: Langevine Thermostat

Hi there, What is the way to use Langevine thermostat in GROMACS. Thanks -- 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 posting! Please don't post (un)

[gmx-users] Reg: Parallel run

Dear Users, I am trying to run my simulation in parallel using above 40 threads on a cluster using qsub system but i am getting the following errors Fatal error: The number of nodes you selected (43) contains a large prime factor 43. In most cases this will lead to bad performance. Choose a n

[gmx-users] Reg: RMSD calculation of a certain portion of protein

Hi All, Is there any way of calculating RMSD of only a certain portion of protein structure after simulation. Like in Amber ptraj utility has this option to mask out certain portion in RMSD. Thanks Rohit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/list

[gmx-users] Putting back the images of residues and atoms in the box

Hi there, I am trying to analyze a trajectory and some of the residues and atoms are seen as the image across the bound is there anyway to put them back in the centre box. Thanks Rohit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

[gmx-users] Reg : Protein-ligand complex using Amber force field

Dear GMX user, Can anyone suggest how to use simulated a protein-ligand complex using AMBER force field in GROMACS. And one thing more in another simulation i am trying to find out the difference in protein complex interaction by mutating one residue. Right now I am using simple procedure to

[gmx-users] Reg : Simulating heterologous protein complex with bound ligand

Dear Gromacs Users, I am working on a protein complex with two subunits which are heterologous and I docked them using HADDOCK. Now, to one of the subunit I built a ligand covalently attached to one of the residue, which enters into the active site of the another subunit in the complex. Now I wa

[gmx-users] Reg : Simulating heterologous protein complex with bound ligand

Dear Gromacs Users, I am working on a protein complex with two subunits which are heterologous and I docked them using HADDOCK. Now, to one of the subunit I built a ligand covalently attached to one of the residue, which enters into the active site of the another subunit in the complex. Now

[gmx-users] Reg: Running gromacs on a condor cluster

Hi everyone.. I just made a small two node condor cluster and was trying to run gromacs on it ... so i used the vanilla environment and placed the gromacs mdrun command in a shell script and used the shell script to run the command ... and it is running also ... but only one one system .. my pool

[gmx-users] Reg: MDS of docked comples

lining residues but for this i don't have any protocol ... therefore if anyone can suggest me a standard protocol for simulating docked compexes along with the mdp files ... then please do suggest ... Regards Rohit -- Rohit Farmer M.Tech Bioinformatics Department of Computational Biolog