[gmx-users] correction in oplsaa to rb conversion?

I just derived the conversion of the dihedral constants from OPLSAA to RB and I get a set of equations different from the ones printed in the manual (3.3, p 56). C1 = V1 / 2 - 3 V3 / 2 C3 = 2 V3 These are the negative of what is printed in the manual. The rest are the same. I'd like to know if

Re: [gmx-users] Hydrogen bonds with version 3.3.1

Gianluca Interlandi wrote: Dear gmx-users, I am trying to calculate hydrogen bonds with gromacs version 3.3.1 I would like to have a cutoff of 2.7 A between hydrogen and acceptor and an angle cutoff of 60 degrees. For that I'm using the following command: g_hbond -f simulation.trr -s

Re: [gmx-users] afm pulling

Hi There seems to be something wrong with your init-vector. Ich have written a small python script, which simply calculates the vector for convenience purposes. You still need the pull- and COM-group coordinates, though. But that shouldn't be a problem. If you want it, I'll send it via mail.

Re: [gmx-users] correction in oplsaa to rb conversion?

gil claudio wrote: I just derived the conversion of the dihedral constants from OPLSAA to RB and I get a set of equations different from the ones printed in the manual (3.3, p 56). C1 = V1 / 2 - 3 V3 / 2 C3 = 2 V3 These are the negative of what is printed in the manual. I think you're

Re: [gmx-users] Hydrogen bonds with version 3.3.1

Dear David, Thanks for your reply, The hbond program is rather complex, but the hbond criterion itself is not (but note that the definition of the angle has changed from 3.2.1 to 3.3, from AHD to ADH). This hasn't been clear to me as the online documentation says DHA: -a real 30 Cutoff

Re: [gmx-users] Hydrogen bonds with version 3.3.1

Gianluca Interlandi wrote: Dear David, Thanks for your reply, The hbond program is rather complex, but the hbond criterion itself is not (but note that the definition of the angle has changed from 3.2.1 to 3.3, from AHD to ADH). This hasn't been clear to me as the online documentation says

Re: [gmx-users] correction in oplsaa to rb conversion?

Hi, On May 2, 2006, at 9:48 AM, David van der Spoel wrote: gil claudio wrote: I just derived the conversion of the dihedral constants from OPLSAA to RB and I get a set of equations different from the ones printed in the manual (3.3, p 56). C1 = V1 / 2 - 3 V3 / 2 C3 = 2 V3 These are the

Re: [gmx-users] popc

Hi!I'm using the popc.top which I have downloaded from this websitehttp://moose.bio.ucalgary.ca/index.php?page=Downloadsand the forcefield I'm using is ffgmx, gromacs forcefield. Cheers,MGOn 5/2/06, mahbubeh zarrabi [EMAIL PROTECTED] wrote: hiI try to use make_hole program to make a hole in

Re: [gmx-users] afm pulling

Thanks Emily and Maik for your feed-back You both are right regarding the init vector. I happened to be the sign of it as Emily guessed. Changing the direction by doing xpull-xref, ypull -yref, zpull-zref and not xref-xpull.works fine. Thanks for the offer on the script though. Thanks

[gmx-users] Highest possible temperature in NPT?

Dear community, I am trying to perform some wild REMD tests, and see the effect of very high temperature on a solvated 100-residue protein.. (hottest replica temperatures of 500-1000K). So far, the simulations would crash whenever using the NPT ensemble.. temperatures would remain correct

[gmx-users] Reaction field: Berendsen or Nose-Hoover thermostat?

Dear community, I am currently running REMD with reaction field. I started with the berendsen thermostat, and my md average temperatures were 10 to 15K warmer than the ones specified in the input file. I had thermostat time coupling constants of 0.1 for the protein and 0.4 for the

[gmx-users] Highest possible temperature in NPT?

It is not immediately clear how one would implement REMD with NPT. In the simplest instance, your monte carlo test would be based on unscaled volumes (that would later scale) and including data from some time period X after a move would lead to a non-maxwellian distribution that was overly spread

Re: [gmx-users] Hydrogen bonds with version 3.3.1

The hbond program is rather complex, but the hbond criterion itself is not (but note that the definition of the angle has changed from 3.2.1 to 3.3, from AHD to ADH). This hasn't been clear to me as the online documentation says DHA: -a real 30 Cutoff angle (degrees, Donor

Re: [gmx-users] Hydrogen bonds with version 3.3.1

Gianluca Interlandi wrote: The hbond program is rather complex, but the hbond criterion itself is not (but note that the definition of the angle has changed from 3.2.1 to 3.3, from AHD to ADH). This hasn't been clear to me as the online documentation says DHA: -a real 30 Cutoff angle

Re: [gmx-users] Highest possible temperature in NPT?

[EMAIL PROTECTED] wrote: It is not immediately clear how one would implement REMD with NPT. In the simplest instance, your monte carlo test would be based on unscaled volumes (that would later scale) and including data from some time period X after a move would lead to a non-maxwellian

[gmx-users] Error in Conjugate Gradient Minimization

Hello, When trying to do CG minimization, I keep getting the following error: Converted 0 out of 0 CUBICBONDS to morse bonds for mol 8 processing coordinates... double-checking input for internal consistency... ERROR: can not do Conjugate Gradients with constraints (12309) There were 3

Re: [gmx-users] Error in Conjugate Gradient Minimization

Arneh Babakhani wrote: Hello, *When trying to do CG minimization, I keep getting the following error:* Converted 0 out of 0 CUBICBONDS to morse bonds for mol 8 processing coordinates... double-checking input for internal consistency... ERROR: can not do Conjugate Gradients with constraints