[gmx-users] when will q4md-forcefieldtools.org be back

Dear gxmers, q4md-forcefieldtools.org is very important for my current project, but has been down for 2 weeks. Does any one has idea when will this website be back? Thank you so much~ yours bob -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Li

[gmx-users] when will q4md-forcefieldtools.org be back

Dear gxmers, q4md-forcefieldtools.org is very important for my current project, but has been down for 2 weeks. Does any one has idea when will this website be back? Thank you so much~ yours bob -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Li

[gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule

Dear gmxers, I am simulating a molecule or about 100 atoms. I doNOT want gromacs calculate ALL intra-molecular electrostatics in this molecule. How to do that? Thank you so~ much. yours bob -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/

Re: [gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule

in other words, I want to just assume ALL intra-molecular electrostatics (charge-charge interaction) in this molecule are 0, instead of calculate them in the simulation. 2015-10-21 8:43 GMT+08:00 li he : > Dear gmxers, > I am simulating a molecule or about 100 atoms. > I doNOT wan

Re: [gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule

the topology. > Whether the result tells you something physically meaningful is up to you. > > Just my two cents > > Victor > > 2015-10-20 19:46 GMT-05:00 li he : > > > in other words, I want to just assume ALL intra-molecular electrostatics > > (charge-charge

[gmx-users] how to fix a molecule's initial configuration

Dear gmxers, I want to fix a molecule's, e.g. octanol's, initial configuration in Gromacs MD simulation. I find some hints at https://www.mail-archive.com/gmx-users@gromacs.org/msg21569.html It reads that, I can apply distance restraint or use RMSD umbrella sampling with PLUMED. I wonder if there i

Re: [gmx-users] how to fix a molecule's initial configuration

:56 GMT+08:00 li he : > Dear gmxers, > I want to fix a molecule's, e.g. octanol's, initial configuration in > Gromacs MD simulation. > I find some hints at > https://www.mail-archive.com/gmx-users@gromacs.org/msg21569.html > It reads that, I can apply distance restrain

[gmx-users] is there martini CG parameters for K+ ion?

Dear gmxers, I am not sure if I'd better post my question here, but the martini forum http://www.cgmartini.nl/index.php/forum does not allow me register and post my question there. I am trying to simulate some KCl solution, but only find martini CG Na+ parameters at http://cgmartini.nl/images/para

Re: [gmx-users] Diffusion coefficient water

I think you could try following things to see if you could get 'better' results 1. use time step of 0.2 or even 0.1 fs 2. try different tau-t and tau-p, e.g. use larger tau-t 3. try different p-coupling methods 2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk>: > D

[gmx-users] Fwd: is there martini CG parameters for K+ ion?

Dear gmxers, I am not sure if I'd better post my question here, but the martini forum http://www.cgmartini.nl/index.php/forum does not allow me register and post my question there. I am trying to simulate some KCl solution, but only find martini CG Na+ parameters at http://cgmartini.nl/images/para

Re: [gmx-users] Diffusion coefficient water

4. you could even try NVT ensemble 2016-08-18 2:25 GMT+08:00 li he : > I think you could try following things to see if you could get 'better' > results > 1. use time step of 0.2 or even 0.1 fs > 2. try different tau-t and tau-p, e.g. use larger tau-t > 3. try dif