Re: [gmx-users] Thermostating in NEMD

2010-11-28 Thread David van der Spoel
On 2010-11-27 23.54, Apoorv Kalyankar wrote: Hi, I was wondering how does a thermostat work in a Non Equilibrium Simulation(NEMD) in GROMACS. Does it subtract out the streaming velocity before applying the thermostat or does it not apply thermostat at all in the direction of the applied

[gmx-users] fix center of mass vs fix residues close to COM

2010-11-28 Thread 哦哦
dear all, I am doing a simluation that I want to fix the center of mass of three protein chains , so that they don`t move to much away , should I fix center of mass of every chains, or fix residues that most close to COM. what is the diffenerces between the two method? and if I want

Re: [gmx-users] Replica exchange

2010-11-28 Thread Mark Abraham
On 28/11/2010 4:49 AM, Sai Pooja wrote: Hi, I am running a script that uses mdrun of gromacs and does replica exchange (not using -replex). The reason is that I want to use different table files for different replicas. However, it seems that I cannot supply unique table names. For example, if

[gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)

2010-11-28 Thread Jignesh Patel
Dear Justin, Thanks for your reply. I have checked whole pdb file. Everything is fine. When I remove phosphorylated serine and use only serine then every thing went fine. co-ordinates for phosphoserine are as per following ATOM 1684 N SEP X 167 27.040 22.580 8.280 1.00 0.00 ATOM