Re: [gmx-users] Free energy of discharging and then recharging not zero

Hi Robert I wouldn't expect that either. Morphing G to A should yield quite reasonable results, cause you just have few dummies in your system. The process, you describe is the way, one would think of, yes. Just to get you right. Are you swithing off charges of a whole base or nucleotide? In t

[gmx-users] QM/MM compilation

Dear all, I would like to install the QM/MM support for gromacs 3.3. According to the wiki page I should follow the instructions in: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/qmmm.html where it says that: "From version 3.3 onwards, the default gromacs distributions support QM

[gmx-users] chirality check

dear gromacs user, i am doing simlation of a small molecules which have chiral corbon. i want to chechk whethere the chirality maintaned during simulation or not, any one sugest me how to check it. thanks sanjay ___ gmx-users mailing listgmx-users@gr

Re: [gmx-users] [ angle_restraints_z ]

Dear Berk, Thanks for the reply. Yes. In fact I made the choice of multiplicity=1 based on the explanation in eq. 4.68: "A multiplicity (n) of 2 is useful when you do not want to distinguish between parallel and anti-parallel vectors." Since my molecule is slightly polar and it may matter whet

RE: [gmx-users] [ angle_restraints_z ]

Hi, I think you do not want to distinguish between parallel and anti-parallel. But in your case using multiplicity 1 or 2 does not matter much. 1000 kJ/mol makes the orientation extremely rigid, but I don't know how rigid you want to have it. 100 kJ/mol is probably a more reasonable order of magni

Re: [gmx-users] chirality check

DIY solution: You can calculate the location of the carbon relatively to a plane defined by three of the atoms bound to the carbon. To be on the safe side, also calculate on which side the fourth atom is located (should be the same as the carbon). - Daniel On May 20, 2008, at 13:19, [EM

Re: [gmx-users] Free energy calculations and speed problems

Just to follow up - the cutoff scheme worked quite well. It gave me energies that were ~1% different from those of the PME calculation, which I think compares quite well. The 10-ps run I attempted now takes 3 seconds, instead of 20 minutes. Thanks to everyone for the suggestions. -Justin Quot

Re: [gmx-users] QM/MM compilation

-- Message: 1 Date: Tue, 20 May 2008 12:52:41 +0200 From: "Ramon Crehuet" <[EMAIL PROTECTED]> Subject: [gmx-users] QM/MM compilation To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Dear all, I wo

Re: [gmx-users] QM/MM compilation

Dear Gerrit, Hitch-hiking with a related issue. I saw on your presentation for the Stanford workshop that GMX can work with DFTB. Is this just planned? Ran. ggroenh wrote: >> -- >> >> Message: 1 >> Date: Tue, 20 May 2008 12:52:41 +0200 >> From: "Ramon Crehuet

Re: [gmx-users] Free energy calculations and speed problems

Justin and Michael, Just to clarify here, I don't think you want the "long cutoff in vacuum" scheme to give you the same results as the "PME in vacuum" scheme. That is, if you use PME in vacuum with a periodic box, you will be including copies of the long-range unscreened electrostatic interaction