Re: [gmx-users] Deshuffling a .gro file

On 3/20/2007 10:03 PM, toma0052 wrote: Hello, I am performing a simulation in parallel on four processors. The simulation seems to run fine, and outputs a shuffled *.gro file. I would like to change the order of atoms to what they were in the original input *.gro file, but I am having some

[gmx-users] parinello-rahman coupling

Dear gmx-users, I am a new one... coming to the point...I am simulating in parallel different configurations and settings of a protein around 300 residues large plus approximately 12000 water molecules. I am simulating NPT with berendsen for P and T to equilibrate over 100 ps and then the simu

[gmx-users] Fwd: Drug - Enzyme Tutorial

Note: forwarded message attached. - Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains.--- Begin Message --- Although I could run sucessfully speptide tutorial,while attempting the drug-enzyme

Re: [gmx-users] parinello-rahman coupling

Hi Loris, Enjoying the nice weather here, I'll just give a gentle reiteration of previous remarks. What you observe is caused by the fact that you only have a very small system from which you try to extract a macroscopic property (i.e. defined only for large systems). The large fluctuations are n

[gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

Note: forwarded message attached. - Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games.--- Begin Message --- Hi! I'm trying to do a simulation of a protein with bound sulfite ion (Tyr (SO3H)).After the first command ( pd

Re: [gmx-users] Fwd: Drug - Enzyme Tutorial

Hi Fulya, Did grompp give you any warnings? At what time did the error occur? At the start of the simulation or later? Could you check the log file for LINCS warnings, and try to track down the first occurrence? This would help to be able to say some more than "your system is exploding". Best,

Re: [gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

Hi Fulya, You can't just simulate everything you set your mind on. There are no parameters for sulfite bound tyrosine in the database (just what it says). You have to add them yourself, which I don't recommend at this point, since it is clear you have but little experience in this field (and para

Re: [gmx-users] parinello-rahman coupling

Hi Tsjerk, Thanks for your prompt reply. I was asking about the average value of the property. I understood that large fluctuations are reasonable, but I was expecting that the mean value over 15 ns could be somehow as the set in the parameter file as happens with Berendsen pressure coupling.

[gmx-users] gen_vel

HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no.AFTER THAT I USED gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT VERY BAD RMSD GRAPHICS.ANY HELP ABOUT WHAT IS THE MEANING OF gen_vel=no,gen-vel=yes?

Re: [gmx-users] parinello-rahman coupling

Hi Lorix, Sorry for that. You used the word "maintained" from which I inferred you were referring to the fluctuations (biased by the occurrence of the question obviously). Under normal conditions the equilibration shouldn't take that long. How far off is the mean? Do you still observe a trend? St

Re: [gmx-users] Fwd: Drug - Enzyme Tutorial

Hi Tsjerk, Many thanks for your suggestions.After "grompp -f em.mdp -c trp_b4em.pdb -p trp.top -o trp_em.tpr " comand there was no warning message.Then I did mdrun ( mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g em.log -e em.edr ) and it was finished but it gave warning message(Warni

Re: [gmx-users] gen_vel

GENERATE VELOCITIES FROM A maxwell DISTRIBUTION FOR ALL ATOMS OR NOT (keep from file or 0.0). SEE CHAPTER 7 OF THE gromacs MANUAL. YOUR WELCOME Tsjerk On 3/27/07, özge kül <[EMAIL PROTECTED]> wrote: HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USE

[gmx-users] Converting CHARMM trajectories (.trj) to GROMACS trajectories (.xtc)

Dear gmx-users, I would like to analyze CHARMM trajectories in GROMACS, and wonder if there are available scripts or tools to convert CHARMM traj to GROMACS traj (.xtc). I've searched the contributed software and forum sections, and it looks like there is a script for that, but couldn't find

Re: [gmx-users] gen_vel

according to what you have described, it is correct. is your reference structure wrong for RMSD calculation? On 3/27/2007 8:56 PM, özge kül wrote: HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no

Re: [gmx-users] Topology file for D2O

Hi Joys Yu, In addition to Tserks comments you might want to use a more specifically developed heavy water model. Here is a reference you may find usefull: An effective pair potential for heavy water - J. Raul Grigera The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp. 8

Re: [gmx-users] Topology file for D2O

Hi, I am not an expert about heavy water -- but it does seem strange to me to think that you could get "heavy water" just by changing the mass of the hydrogens in a conventional water model. The *only* thing this will affect is the kinetic energy and mass of water. Presumably changing hydrogen to

Re: [gmx-users] parinello-rahman coupling

Hi Tsjerk, I set the pressure in the parameter file to be 1bar and I get different average values ranging from 0.4 to 1.7 bar. Maybe they are not significantly different (?) but I try to simulate large conformational changes and according to what I saw small difference in settings can make diff

Re: [gmx-users] parinello-rahman coupling

Hi Loris, You're always stuck with limitations of simulations one way or the other. Now, berendsen barostat is disputed in some sense, but it does a good job usually (and it is so simple). The question would be, how far off is it from THE thermodynamic ensemble of your system (and how far off are

Re: [gmx-users] gen_vel

? wrote: HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no.AFTER THAT I USED gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT VERY BAD RMSD GRAPHICS.ANY HELP ABOUT WHAT IS THE MEANING OF gen_vel=no,gen-vel=

[gmx-users] tabulated nonbonded interactions and free energy calculations

All, I'm trying to figure out how to use tabulated nonbonded interactions in GROMACS in conjunction with free energy calculations. While the documentation addresses both separately, I am somewhat confused about what would happen if I try to use both simultaneously. In particular, I'm looking at t

Re: [gmx-users] Converting CHARMM trajectories (.trj) to GROMACS trajectories (.xtc)

Hwankyu Lee wrote: Dear gmx-users, I would like to analyze CHARMM trajectories in GROMACS, and wonder if there are available scripts or tools to convert CHARMM traj to GROMACS traj (.xtc). I've searched the contributed software and forum sections, and it looks like there is a script for that

Re: [gmx-users] Carbon Nanotube Simulations

Hi, Actually, I believe that only one force field (ffgmx) currently has an n2t file, at least as recently as 3.3.1. I would try running a find or locate command to see if you even have the n2t files to begin with. I also believe I read earlier on the mailing list that the CVS branch has some im

[gmx-users] Incorrect dihedral restraints

Hi, i've solved my problem concerning dihedral restraints, hope that it'll be usefull for those who have trouvble using it. The constraints must have values between 0 and 360° ! Not that complicated, but it took me 2 weeks to figure that out... ___ gmx-

Re: [gmx-users] Deshuffling a .gro file

Hi, Thanks for the response. Sorry that the statement of my problem was so cumbersome. My problem was with the noncontinuous numbering of molecules following deshuffling using editconf. What I am doing, is following an md run, performing a simple transformation of the coordinates in the res

[gmx-users] help with g_sdf

Hi Please can someone help me with g_sdf I would like to calculate the sdfs of two different types of lipid headgroups around another species in my system. Specifically I have 119 lipids of one type and 116 of the other- do I need to normalise to account for this difference? If so, any advice as

[gmx-users] Topology file for D2O

Dear all, Thank you so much for your suggestions. You don't know how much you guys are helpful. First with Tsjerk's suggestion of using gmxdump, I got to know where the problem is. What I changed is ffgmx.atp and spc.itp. It is useful to pdb2gmx. But for grompp, it is not enough. I have to change

RE: [gmx-users] help with g_sdf

> Please can someone help me with g_sdf > I would like to calculate the sdfs of two different types of > lipid headgroups around another species in my system. > > Specifically I have 119 lipids of one type and 116 of the > other- do I need to normalise to account for this difference? > If so, a

[gmx-users] How to turn off Langevin thermostat for NVE Simulation

Hi, I would like to run NVE Simulation and so I turn off the Temperature coupling (Nose-Hoover or Beredsen). Yet I guess the Langevin thermostat coupling is still on (From the manual, in .mdp file, for Langevin Dynamics, if bd_fric is set to be zero, the friction coefficient for each particle is

Re: [gmx-users] Deshuffling a .gro file

toma0052 wrote: Hi, Thanks for the response. Sorry that the statement of my problem was so cumbersome. My problem was with the noncontinuous numbering of molecules following deshuffling using editconf. What I am doing, is following an md run, performing a simple transformation of the coor

[gmx-users] Carbon Nanotube Simulations

Hi, I added CNT residue in the ffgmx.rtp as follows: " [ CNT ] [ atoms ] C C0.00 0" Then I used x2top to gene

[gmx-users] Generating carbon nanotubes for GROMACS

Hi, I am using Tubegen to generate carbon nanotubes for my simulations. Is there any better method to do this? Thank you very much, George ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

Hi Tsjerk, Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly. And I dont think there is a problem with the mail s

Re: [gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

fulya caglar wrote: Hi Tsjerk, Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly. It's an involved process, which va

Re: [gmx-users] g_rdf normalisation

2007/3/26, syma <[EMAIL PROTECTED]>: Hi, I am attempting to calculate the rdfs of the various components of my system wrt to DNA phosphate groups. However, I was wondering how I can normalise so I can compare the various rdfs? Ideally I would like to have the g(r) normalised in the range 0-1.