[gmx-users] is it any serious error

hello all... when ever i run simulation i'm getting this kind of out put saying there is one warning as shown below Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file

[gmx-users] simulating the effect of Ph

hello all... i know simulating the effect of temperature and pressure on the protein is there any way to study the effect of Ph on the system -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] is it any serious error

Bharath.K. Chakravarthi wrote: hello all... when ever i run simulation i'm getting this kind of out put saying there is one warning as shown below Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening

Re: [gmx-users] simulating the effect of Ph

Bharath.K. Chakravarthi wrote: hello all... i know simulating the effect of temperature and pressure on the protein is there any way to study the effect of Ph on the system That is a complex question, but there are a number of useful discussions about this in the list archive. The

Re: [gmx-users] conversion of desmond trajectory files into gromacs

Really? This is really great! Is there any need to specify the location of the vmd libraries? If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this somehow still possible? On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote: In case you use the GIT version of the analysis

[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Thanks for helping! Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Position your solutes using editconf -center, then add solvent. -Justin Thanks for helping! Rasoul

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? Rasoul On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear All, Hello I understand

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is

[gmx-users] manual eq. 4.74-4.75 (dihedral restraints) head scratcher

Hello gmx-users, you rock and rollers, Equations 4.74 and 4.75 in my copy of the manual have (please pardon my pseudo-LaTeX): (4.74) \phi' = (\phi - \phi_0) MOD 2\pi (4.75) V(\phi') = \frac{1}{2}k ( \phi' - \phi_0 - \Delta \phi )^2 if \phi' \Delta \phi or V(\phi') = 0 if \phi' \leq

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Thanks for the information. Because of haven't satisfactory model from my co-solvent and I have to add it randomly along with the solvent by genbox -ci -nmol. the reason of this criteria relate to crash of system (solute+co-solvent+solvent) in the first step of simulation, because small distance

Re: [gmx-users] conversion of desmond trajectory files into gromacs

On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole x.peri...@rug.nl wrote: Really? This is really great! Is there any need to specify the location of the vmd libraries? By default it tries to find them at /usr/local/lib/vmd/plugins/*/molfile If you have them installed somewhere else you can