Re: [gmx-users] interfacing with Gaussian 09

Sorry I forgot to change the subject line on my previous message; it was inadvertent. If Gerrit gets these emails maybe he can tell me what I'm doing wrong. Here are the symptoms: I'm using the gau script and I think the program is executing through until at least line 177 of the qm_gaussian.c

Re: [gmx-users] interfacing with Gaussian 09

Hi, Please don't subscribe to a digest if you're planning to reply to the digest and de-thread the discussion. Gerrit said the other week that gau works. Mark On Fri, 10 Jun 2016 18:18 Mark Abraham wrote: > Hi, > > Please check out

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 49

Have you ever heard of anyone successfully using the gau script available at http://wwwuser.gwdg.de/~ggroenh/qmmm.html? I don't have access to the Gaussian source code and cannot create the modified links. However, according to the link I just cited, it can be done without modifying links.

[gmx-users] Open-closed transition in a dimeric enzyme, WTM simulations

Dear All, I am studying an enzyme where the closing of a loop should happen upon ligand binding to the active site. In unbiased simulations, even after 300 ns of simulation time the loop does not close the reaction center. Thus, we realized that the open-closed conformational change may have a

[gmx-users] problem compiling template

Hi, I just installed a pristine gromacs 5.1.2, on my lubuntu 64bit vanilla desktop, as in: prompt> cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.2-bin -DGMX_BUILD_OWN_FFTW=ON prompt> make -j 6 prompt> make install this worked ... then if I go to the resulting

[gmx-users] Problem understanding internode communication

I am new here so it may be a childish question, but I wanted to understand how the nodes communicate atom information and force calculations.To that end I started going through the source code (version 5.1.2 and 4.5.4) but I am losing track of the functions. If you could point out the functions

Re: [gmx-users] interfacing with Gaussian 09

Hi, Please check out http://wwwuser.gwdg.de/~ggroenh/qmmm.html and http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM Mark On Fri, Jun 10, 2016 at 5:13 PM Clinton King wrote: > I'm having difficulty interfacing GROMACS with Gaussian 09. Is

Re: [gmx-users] how to freeze an arbitrary set of atoms

Hi, This is called an index group (see manual) and can be made by hand, or with gmx make_ndx, or gmx select, in increasing order of powerfulness. :-) Mark On Fri, Jun 10, 2016 at 3:26 PM Irem Altan wrote: > Hi, > > I would like to freeze a subset of protein atoms in my

Re: [gmx-users] using trjconv while the simulation is still running

Hi, Sure. Or if you want to feel safer, make a copy of the file first. Mark On Fri, Jun 10, 2016 at 5:42 PM Irem Altan wrote: > Hi, > > Is it possible to use trjconv while the simulation is still running? I > want to double check that the position restraints are working

[gmx-users] using trjconv while the simulation is still running

Hi, Is it possible to use trjconv while the simulation is still running? I want to double check that the position restraints are working as expected, without having to stop and re-start the simulation. Best, Irem -- Gromacs Users mailing list * Please search the archive at

[gmx-users] interfacing with Gaussian 09

I'm having difficulty interfacing GROMACS with Gaussian 09. Is there anyone who has successfully done it who is willing to give some advice? -- Clinton King Graduate Student Chemistry Department Brigham Young University -- Gromacs Users mailing list * Please search the archive at

[gmx-users] how to freeze an arbitrary set of atoms

Hi, I would like to freeze a subset of protein atoms in my system. Since I don’t want to freeze them all, I can’t really do the following: freezegrps = Protein-H freezedim = Y Y Y How can I define a custom set, e.g. atom indices {400,1200,234} etc.? Best, Irem -- Gromacs Users

Re: [gmx-users] minor edits to a .gro file

Agreed! I have had some success using umbrella sampling, but the reaction coordinate is quite tricky and prone to periodic boundary artefacts. I’m putting together a script to strip out the force entries where the corresponding frame demonstrates the long fibril protein seeing itself in addition

[gmx-users] Missing oxyz in vmx distance output

Hi all, I¹m really hoping this is my own oversight. Using Gromacs 5.0.4 (can¹t upgrade, this is a distribution on a cluster) I can generate each of the output options (-oav -oall -oh -oallstat) apart from -oxyz when I run the command: gmx_d distance -f NPT_0_40ns_compress.gro -s

Re: [gmx-users] minor edits to a .gro file

Hi, I certainly haven't tried something as complicated as taking three fragments, some charged, and morphing them to a neutral structure, but I would consider very seriously doing it in several stages, e.g. breaking into neutral fragments, dissociation of fragments, charging of fragments. Mark

Re: [gmx-users] minor edits to a .gro file

Hi Mark, I had considered (and I still am) defining a distance constraint between the lysine-N and arginine-N-N on their sidechains, which defines the points where the morphing into a bond formation would be. I am essentially trying to morph back and forth into this structure:

Re: [gmx-users] minor edits to a .gro file

Hi, One generally uses distance restraints to limit the sampling space of the separated amino acids, but exactly how to implement that might take a bit of iterating. GROMACS 5.1 can do inter-moleculetype restraints, but that probably isn't necessary/useful in this context. Mark On Fri, Jun 10,

Re: [gmx-users] minor edits to a .gro file

James and Justin, Thanks for your suggestions. This was ultimately to hack around with the PMX toolkit for making dummy atoms in preparation for free energy calculations. Unfortunately, I’m back to the drawing board (likely to be umbrella sampling) as an alchemical morphing of a glycated cross

[gmx-users] 答复: simulation with new force field

Thanks. Do you know whether is there any other package that is more appropriate to handle this problem ? 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 David van der Spoel