[gmx-users] a question about potential energy

pHi, all/ppI have found a problem thatnbsp;in my Md run the potential energy in every frame was about -9e+04 while the average potential energy of all wasbr /-1.88e+02. What is wrong with it? Why are they so different? Can anybody tell me the reason? Thanks!/pppS: the attachement is the md.log.

Re: [gmx-users] Suggestion needed for new workstation

Am Donnerstag, 9. August 2007 schrieb james zhang: Hi James I want to buy a new workstation for MD simulation. I think the Mac Pro from Apple is really nice. Workstations are imho not best if you plan to do long-taking simulations. Only think about this option if you're doing really short

Re: [gmx-users] Suggestion needed for new workstation

Hi, On Friday, 10. August 2007 09:29, Martin Höfling wrote: Am Donnerstag, 9. August 2007 schrieb james zhang: Hi James I want to buy a new workstation for MD simulation. I think the Mac Pro from Apple is really nice. Workstations are imho not best if you plan to do long-taking

Re: [gmx-users] doing simplest simulations

Hi again, I re-did my simulations with the posted .mdp-file. The huge differences to my formerly posted file are a few vanished semicolons, and after a fine simulation-run an added dispersion correction due to a pressure that was slightly higher than expected. Did't really help, made it

Re: [gmx-users] Pull code with shuffle/sort options

Thank you Chris for providing recognition of this issue. -Steve Chris Neale wrote: I have encountered noticeable differences while using the pull code with the -shuffle -sort options in parallel, as opposed to running in serial or in parallel without the options. Using -shuffle -sort, the

Re: [gmx-users] Storage of large output files

Am Donnerstag, 9. August 2007 schrieb Monika Sharma: Here, We first thought about our own backup system but the local computing center provides a nice backup infrastructure based on Tivoli, so asking there would be worth a try. The gui-client is ugly but dsmc works fine and can be used from

Re: [gmx-users] Re: question about free energy. Gromacs user

Thank you David and Arneh for the comments. I just have a couple of things i want to clarify about the constrain distances i used. The distance I used to pull the ligand and receptor apart was a non-bonded distance between the amide nitrogen of the ligand and the oxygen carbonyl of the receptor

Re: [Bulk] [gmx-users] a question about potential energy

Hi, You shall help yourself to find the answer by plotting your energy with g_energy. Have your equilibrated your system well? Which stage of simulation are you running with, em, eq or production run? Having large fluctuation is sometimes normal and sometimes bad. Also, please attach necessary

[gmx-users] a basic question

Hello everyone, I met with a problem today. I tried to simulate dppc lipid in water.However, when I want to minimize energy ,the grompp showed the error message like this: number of coordinates in coordinate file (box.gro 8253 ) doesn't match topology ( topol.top , 0 ). I have used gromacs for

Re: [gmx-users] a basic question

Why you put a none in the include? It doesn't mean none when there is an none. Regards, Yang Ye On 8/11/2007 11:36 AM, Q733 wrote: Hello everyone, I met with a problem today. I tried to simulate dppc lipid in water.However, when I want to minimize energy ,the grompp showed the error message

[gmx-users] a basic question

Hello everyone, I met with a probelm today.I want to simulate dppc lipid in water, however when I want to do energy minimization the grompp displayed number of coordinates in the coordinate file (box.gro, 8253) does not match topology (topol.top, 0).I have checked the input file several times