Re: Fwd: [gmx-users] Hen egg white lysozyme.

2006-08-16 Thread David van der Spoel
Viswanadham Sridhara wrote: Hello Dr.Spoel and others, There is one more problem with the simulation of hen egg white lysozyme simulation in water I am running. The timestep I could use is just 0.5 fs or 0.0005ps. Is there any way around to increase the timestep. This is how a part of my mdp f

Re: Fwd: [gmx-users] Hen egg white lysozyme.

2006-08-15 Thread Viswanadham Sridhara
Hello Dr.Spoel and others,There is one more problem with the simulation of hen egg white lysozyme simulation in water I am running. The timestep I could use is just 0.5 fs or 0.0005ps. Is there any way around to increase the timestep. This is how a part of my mdp file looks like:; RUN CONTROL PARAM

Re: Fwd: [gmx-users] Hen egg white lysozyme.

2006-08-11 Thread Viswanadham Sridhara
Hi David.I thought of the same and I started running it using angular mode yesterday.Thanks though for a quick feedback.-VissuOn 8/11/06, David van der Spoel <[EMAIL PROTECTED]> wrote:Viswanadham Sridhara wrote: > Hello everyone,> I could figure out that parameters for NAG are not that important.

Re: Fwd: [gmx-users] Hen egg white lysozyme.

2006-08-11 Thread David van der Spoel
Viswanadham Sridhara wrote: Hello everyone, I could figure out that parameters for NAG are not that important. So, I used free HEWL. I started running it, but I realize that the protein started to rotate around the center of mass with a frequency of around 200ps. I used "Linear" as an option fo

Fwd: [gmx-users] Hen egg white lysozyme.

2006-08-11 Thread Viswanadham Sridhara
Hello everyone,I could figure out that parameters for NAG are not that important. So, I used free HEWL.I started running it, but I realize that the protein started to rotate around the center of mass with a frequency of around 200ps. I used "Linear" as an option for comm_mode and I used "Protein" i