Re: [gmx-users] water in lipid bilayer

Do you mean constrain the force constants just in the z-direction? Keep in mind that the water is already in the gap, so it's now a matter of getting it out. Would constraining water in any direction accomplish this? Thanks, Max On Nov 19 2007, himanshu khandelia wrote: I already constrain

Re: [gmx-users] water in lipid bilayer

eventually make their way out during the course of the simulation. Many thanks, Max On Nov 19 2007, Mark Abraham wrote: N-J.M. Macaluso wrote: Hi, I'm performing a transmembrane protein simulation in an explicit DPPC bilayer. I manually removed the lipids to accomodate my protein and

[gmx-users] water in lipid bilayer

Hi, I'm performing a transmembrane protein simulation in an explicit DPPC bilayer. I manually removed the lipids to accomodate my protein and the system has undergone 15 ns of equilibration. In removing the lipids, I a gap betwteen the protein and membrane resulted. Most of the lipid molecul

[gmx-users] protein/membrane simulation parameters

Hi, I have two questions that may seem quite simple, but I haven't found clear answers to them. It has to do with the md simulation parameters of a solvated protein/membrane system. The first question is about temperature. Some papers simulate at 300 K, others at 298 K, and others at physiol

[gmx-users] problem with waters in protein/membrane simulation

Hello, I'm having a small but significant problem with simulating a protein inserted in a DPPC membrane. I have simulated the system for 15 ns with position restraints on the protein to allow the lipids to anneal around it, but have recently found a small problem. I found a small gap between t

[gmx-users] area per lipid

Hi, Is there a Gromacs command for calculating the area per lipid after a membrane simulation? Thanks, Max Macaluso ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] publishing with development version of Gromacs

Hello, I am running protein simulations in an explicit membrane environment, and have found that the CVS development version of Gromacs works much faster than the released version. Is it okay to publish simulations performed on the development version? What kind of validation would I need if I

Re: [gmx-users] restarting a run using tpbconv

/2007 10:15 PM, N-J.M. Macaluso wrote: This may be a trivial question, but how do you save velocities in this case? Would it be in the .mdp file or in the tpbconv command? Thanks for your help, Max On Jul 21 2007, David van der Spoel wrote: N-J.M. Macaluso wrote: Hello, I am running a very

Re: [gmx-users] restarting a run using tpbconv

This may be a trivial question, but how do you save velocities in this case? Would it be in the .mdp file or in the tpbconv command? Thanks for your help, Max On Jul 21 2007, David van der Spoel wrote: N-J.M. Macaluso wrote: Hello, I am running a very long simulation, and the cluster

[gmx-users] restarting a run using tpbconv

Hello, I am running a very long simulation, and the cluster I'm using has a wall time. I am using tpbconv to restart my simulations from a frame in the last run, but this doesn't seem to be working. When I analyze the second trajectory, the starting structure looks identical to the starting

[gmx-users] REMD log files

Hi, Thanks for your previous responses to my questions on REMD. I have a general question about understanding REMD in gromacs. Can someone break down how to read the .log file? For instance, one of the main goals I have is to graph the time evolution of temperature exchange for a specific

[gmx-users] TREMD in development version

Hi, I have a question regarding the implementation of temperature replica exchange MD (TREMD) in the development version of Gromacs. Is it possible to simulate more than one replica on one processor? As far as I know, the distributed version 3.3 can only accept one replica per processor.

[gmx-users] Question on analyzing REMD simulation

Hello, Thanks for your responses on the demux.pl script. I have some more basic questions on how to analyze an REMD simulation in Gromacs. (1) How can I find the acceptance ratio? (2) Does anyone know how to graph the temperature or potential energy of a single replica as a function of ti

[gmx-users] how to use demux.pl for REMD analysis

Hello, I've been reading all of the archived questions on the analysis of REMD in Gromacs, and I'm still a bit confused. It appears that the first step is to use the demux.pl script to demultiplex the REMD trajectories. How to use this script, and what exactly this is supposed to accomplis

Re: [gmx-users] how to submit replica exchange MD simulation

score). If I install the latest CVS version ( 3.399), is it possible to run replica exchange in an score environment, or do I still need LAM? Also, is REMD implemented differently in the CVS version? Thanks, Max Macaluso On Apr 9 2007, David van der Spoel wrote: N-J.M. Macaluso wrote: Hello

[gmx-users] how to submit replica exchange MD simulation

Hello, I have a question regarding replica exchange MD in Gromacs. I think I am preparing all of the files in the correct fashion, but I continually get the same error message. Here is what I'm doing. I prepared three different mdp files, each specifying a specific temperature (PME0.mdp,