[gmx-users] segmentation fault at middle of MD run

Dear gmxions, In my simulation of protein for 2ns crashed at around 850ps and core dumped. Earlier run of simillar system was smooth for 2ns. This time I just copied the final full.tpr and full.mdp to different machine but same os(Cygwin under windowsXP) to run the sim

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

> But now for the most important question: is there a reproducible problem with > the angle? Yes. I include everything into a tar: http://biocroma.unizh.ch/gianluca/Files/Gromacs/hbond.tar.bz2 I'm using the following command to verify if the hydrogen bond "ARG 552 HH12 - GLN 548 OE1" is formed

Re: RE : [gmx-users] segmentation fault in mdrun when using PME

Hello, I'm experiencing the exact same problem, when trying to do some restrained molecular dynamics of a small peptide in a water box. Have you had any luck in trouble-shooting this? (I've pasted my mdp file below, for your reference).  Also running Gromacs 3.3.1 Arneh title = ResMD warnings

Re: [gmx-users] grompp: Atoms in the .top are not numbered consecutively from 1

D. Ensign wrote: Greetings. I'm having a lovely time with my old pal grompp, except for the grumpiness after replacing eight water molecules with ions in my system and discovering -- to my astonishment -- the following message: "Atoms in the .top are not numbered consecutively from 1" Well,

[gmx-users] grompp: Atoms in the .top are not numbered consecutively from 1

Greetings. I'm having a lovely time with my old pal grompp, except for the grumpiness after replacing eight water molecules with ions in my system and discovering -- to my astonishment -- the following message: "Atoms in the .top are not numbered consecutively from 1" Well, this is interesting

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

Thank you for your input, I fixed it. You need to include: define = -DFLEXIBLE in the mdp file. Arneh Mark Abraham wrote: 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 m

[gmx-users] Error installing gromacs on solaris system

Dear all, I got the following error message while trying to install gromacs on a cluster running on solaris operating system. FFTW installed successfully. Could anyone help ?Undefined   first referenced  symbol in file__floatdidf  

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 (123

[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 warni

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 distributi

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 (degre

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 an

[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 t

RE : [gmx-users] segmentation fault in mdrun when using PME

De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it

[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 solvent

[gmx-users] Nose-Hoover and REMD restarts?

Dear community, I have been performing some Nose-Hoover REMD trial runs.. I just wanted to check out 1) whether these two are compatible, and 2) whether it is possible to restart the REMD simulation giving the Nose-Hoover phase of the previous run. How can that be done? tpbconv -e ener

[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 b

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 Em

Re: [gmx-users] popc

Ooops!I mean, I'm using popc.itp, of course!bye,MGOn 5/2/06, MGiò <[EMAIL PROTECTED]> wrote: Hi!I'm using the popc.top which I have downloaded from this website http://moose.bio.ucalgary.ca/index.php?page=Downloadsand the forcefield I'm using is ffgmx, gromacs forcefield. Cheers,MGOn 5/2/06, mahbub

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 POPC

[gmx-users] popc

hi I try to use make_hole program to make a hole in POPC. how can i make popc.top?what is forcefield for popc in gromacs? thanks zarrabi __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _

Re: [gmx-users] 256 DPPC bilayer

Hi, On May 2, 2006, at 1:01 PM, MGiò wrote: Hi all! I'm desperately looking for a big DPPC bilayer, more than 200 DPPCs. I've read on the mailing list that a 256 lipid bilayer by Lindhal exists, where may I find it? Is it freely downloadable? You can find all files necessary to simulate a

[gmx-users] 256 DPPC bilayer

Hi all!I'm desperately looking for a big DPPC bilayer, more than 200 DPPCs. I've read on the mailing list that a 256 lipid bilayer by Lindhal exists, where may I find it? Is it freely downloadable?Thanks for any help, MG ___ gmx-users mailing listgmx-

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 nega

Re: [gmx-users] fudgeLJ / fudgeQQ are multiplicative factors

[EMAIL PROTECTED] wrote: Perhaps someone can add this to the next update of the manual (on page 101?) Without going to Jorgensen's 1988 JACS paper it is difficult to be sure that fudge means multiply and not divide, especially given the most common usage of the word "factor" and that e.g. Berger

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 D

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] 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 righ

Re: [gmx-users] problem with ffamber94bon.itp

Berk, you're right. That's the way it goes... I think, Eric Sorin mentioned that on his page, though. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 23

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] 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 topol.t