[gmx-users] double-checking

Dear Users, I am trying to simulate Drug - Enzyme Complex accoring to "GROMACS Tutorial for Drug - Enzyme Complex" with different enzyme (ALKALINE PHOSPHATASE FROM HUMAN PLACENTA - ZEF1) and ligand. After adding water with genbox I run: grompp -f em.mdp -c trp_b4ion.pdb -p trp.top -o trp_b4i

[gmx-users] Re: gmx-users Digest, Vol 37, Issue 18

Hi Tsjerk and gmx-users, Thank you for the response. And I will be more clear in asking questions. The force field I am using is ffgmx. I am not sure I will obtain good properties for my system with ffgmx at this time. But I want to understand how to set up my simulation wh

[gmx-users] Positive Potential Energy

Hi, I am running a carbon nanotube in water simulation. I set the reaction field dielectric constant (epsilon_rf) to 80 (that of water) and the dielectric constant (epsilon_r) to 1. The energy minimization (which ignores the temperature coupling) runs well and I get a negative potential e

Re: [gmx-users] g_sas

Hi Arthur, I think it's stated in the header of the .xvg file. Otherwise, it is in the archives, where I just had a glance to revive my memory a bit. It's something like: time hydrophobic-SAS hydrophilic-SAS total-SAS hydration-free-enthalpy Cheers, Tsjerk On 5/4/07, Arthur Roberts <[EMAIL PR

[gmx-users] g_sas

This is a question about what the lines from the solvent accessibility mean. I executed the following command. g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg xmgrace -nxy mdrun.xvg I get two sets of values: one is bigger (black) than the other (red). Is the red lower value, the standard erro

Re: [gmx-users] Question on [ angles ] in topology file?

Try angle restraints. Regards, Yang Ye Chze Ling Wee wrote: Hi GMX users - In the [ angles ] section of the topology file for a protein, is there a minimum or maximum angle value that can be specified i.e. [ angles ] ; i jk funct angle force.c. 1 2 3 1x 250 Is there

Re: [gmx-users] Question on [ angles ] in topology file?

Chze Ling Wee wrote: Hi GMX users - In the [ angles ] section of the topology file for a protein, is there a minimum or maximum angle value that can be specified i.e. [ angles ] ; i jk funct angle force.c. 1 2 3 1x 250 Is there a range of values x can take? Can x be n

[gmx-users] Question on [ angles ] in topology file?

Hi GMX users - In the [ angles ] section of the topology file for a protein, is there a minimum or maximum angle value that can be specified i.e. [ angles ] ; i jk funct angle force.c. 1 2 3 1x 250 Is there a range of values x can take? Can x be negative? Are x = -90 an

RE: [gmx-users] Temperature increase

Dear Mark, thank you very much for prompt reply, I am sorry but I did mistake in my first e-mail I have run an NVE simulation of decamer of glycin first with PBC (coulombtype=PME)and later without PBC (coulombtype=Cut-off). Zuzana -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL P

Re: [gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

Hi Arun, You have to get your methods straight.., and be more clear in the phrasing of your question. I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the cosurfac

[gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

Dear gmx-users: I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the cosurfactant is fatty alcohol. water is of spc model. I got topologies from Prodrg for my surfactan

Re: [gmx-users] Unable to swith from NVT to NPT

Mark Abraham a écrit : Stéphane Téletchéa wrote: I'm probalby doing something wrong but since neither the manual nor the mailing list has driven me to the correct answer, i'm asking you the problem. Thanks in advance for you answers and time. ... Using grompp here and supplying an energy fil

[gmx-users] Energy conservation of crystal surface

Hello gmx-users! Sorry that I am bothering you all the time with energy conservation issues but this time I have problems with a crystal surface consisting of infinite polymer chains. I think that simulation and interaction parameters employed should be conserving the total energy: time step o

[gmx-users] RE: Energy conservation in collision

Hello gmx-users! I am still struggling with the energy conservation in the system where a water droplet (consisting of rigid molecules) collides with a frozen structured surface. The total energy is well conserved at the beginning of NVE simulation when the droplet is appro

Re: [gmx-users] xmgrace

Hi, On Thursday, 3. May 2007 22:07, Michal Walczak wrote: > Dear Gromacs users, > > I'd like to ask if anyone could tell me how to open *.rms file in xmgrace, > if it's possible of course or how to convert such a file into *.xvg? That > *.rms file is an output from NWChem. open it with your favou