RE: [gmx-users] SGI installation problem

Hi, Thanks to David for his suggestion. Now I have the following error. It is a bit of shame that I am hassling you, but I want GMX to work on my sgi. Cheers, Siavoush Here is the error message: gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_spatial.o cc-1028 cc: ERROR File

Re: [gmx-users] g_msd, REMD, trestart...

Julián GC wrote: Thanks for your help, Mark. I cannot demux the trajectories, because I'm running each box at with a different temperature and with a different initial configuration (appropiate to that temperature) (This, combined with the replica exchange, is usually called "parallel temper

RE: [gmx-users] Force field

Dear Nihar, if you contact me off the list I could send to you itp files for native alpha, beta, and gamma cyclodextrins compatible with the gromos forcefield (the ones we used in "jpcb (2007) 4383" and "jpcb (2007) 12625"). Unfortunately I do not have the thioflavin. Regards, Angel Piñeiro. --

[gmx-users] g_msd, REMD, trestart...

Thanks for your help, Mark. I cannot demux the trajectories, because I'm running each box at with a different temperature and with a different initial configuration (appropiate to that temperature) (This, combined with the replica exchange, is usually called "parallel tempering"). Checking the

[gmx-users] Re: kinetically trapped in a local minimum???

Hi Cong: To expand on Mark's answer, there is no "universal test" for convergence of all properties, and therefore the best you can ever hope to do is check for convergence of the observable(s) you care about, and any closely related quantities you can think of (especially, as previously menti

Re: [gmx-users] SGI installation problem

Siavoush Dastmalchi wrote: Hi there, This is a bit funny that I am posting this problem again, but I am hopping that I may find a solution. I recently down loaded gromacs-3.3.3 and was trying to install it on my sgi computer. I get error massage (as shown below). It seems that many others also

RE: [gmx-users] kinetically trapped in a local minimum???

Dear Mark, Thank you very much for your valuable advice. Best regards, Tri From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Sat 3/15/2008 8:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] kinetically trapped in a local minimum???

[gmx-users] SGI installation problem

Hi there, This is a bit funny that I am posting this problem again, but I am hopping that I may find a solution. I recently down loaded gromacs-3.3.3 and was trying to install it on my sgi computer. I get error massage (as shown below). It seems that many others also had such a problem, so won

Re: [gmx-users] kinetically trapped in a local minimum???

#NGUYEN CONG TRI# wrote: Dear Gromacs users, How can we know that the system is properly equilibrated or whether we should extend the equilibration step. Someone suggest that we look at the potential energy to see whether it has converged? Is it correct? That's one test. You should look for

[gmx-users] Force field

Hi GROMACS users, I would like to study cyclodextrin + Thioflavin T in water. Is there any forcefiled parameters for these in any of the force-field supplied with GROMACS? It will be extremely beneficial if anybody can supply field compatible with GROMACS OR force-field parameters for CHARMM li

[gmx-users] kinetically trapped in a local minimum???

Dear Gromacs users, How can we know that the system is properly equilibrated or whether we should extend the equilibration step. Someone suggest that we look at the potential energy to see whether it has converged? Is it correct? One more question, normally, we carry out the equilibration at

Re: [gmx-users] Whereabouts of NDLP???

Hi Alan, Unfortunately there have been server problems (severe hacking) in Groningen some while ago, and the NDLP server was terminated. But, we're right about to reestablish an improved server here in Utrecht. This server will be much faster, seconds rather than hours - the optimal packing for th