Re: [gmx-users] GROMACS on CYGWIN

Also, use the 'nice' command to run gmx at high priority, and switch off CPU frequency scaling. For me, cygwin performance is pretty much the same as that on linux, which is to be expected since most of the code isn't dependent on system calls. Apparently, the only difference you should be able to

Re: [gmx-users] error in hydrocarbon dihedrals of opls-aa?

Dear Markus, Just a follow-up: how did it all end, were able to find the source of error (if any)? 2010/5/10 Markus Tusch > Am 07.05.2010 16:03, schrieb David van der Spoel: > > On 5/7/10 8:45 AM, Markus Tusch wrote: >> >>> Hi everybody, >>> >>> I've just compared the following opls-aa torsion

[gmx-users] NPE simulations: where does all the energy go?

Dear colleagues, There is probably some stupidity involved in my question, but I want to use GROMACS to explore water phase equilibria using the phase coexistence technique. This means that my simulation cell contains a liquid slab and an ice slab in contact, and what I'm trying to do is to see wh

Re: [gmx-users] visualization tool for windows

Have you tried loading the .gro into VMD first? VMD requires it to understand the contents of your trr/xtc files. I believe that VMD can sometimes find it automatically, but sometimes it can't, and you have to first load it and then load the trajectory. Otherwise, you can trjconv your trajectory to

Re: [gmx-users] Gromacs using MKL with Intel 11.1 compilers

Hi, > Anybody have any real-world comparisons of using MKL vs. FFTW3? > http://www.quantumespresso.org/user_guide/node16.html says: Axel Kohlmeyer suggests the following (April 2008): "(I've) found that Intel is now turning on multithreading without any warning and that is for example why their

[gmx-users] Regarding the 'hangs at "atom 0"' issue with x2top 4.x

Hi all, I've recently managed to reproduce the bug with x2top 4.x hanging at "atom 0". The halt occurred when I was trying to generate a topology with the "-pbc yes" option (which is the default used unless you specify otherwise) using a structure file containing no information on the periodic box

Re: [gmx-users] Re: CNT

Hmm... I've been using the 4.0.4 x2top to create OPLS-AA topologies for, e.g., graphane, and it worked more or less right "out of the box", giving very convincing results. What's the problem exactly about recent versions of x2top? I use the -noparams option to leave everything having to do with num

Re: [gmx-users] Re: Groups based on distance criteria

2009/7/20 Vitaly V. Chaban > Hi Matteus, > > Yeah, dynamic groups would be a powerfull tool. But such mechanism is still > under development if I am not out-of-time. > > The possible way to proceed with such kind of research (as Berk advised me > here long ago) is to sort the trajectory (trjorder

[gmx-users] x2top and OPLS-AA vs. fudged 1-4 interactions

Dear colleagues, I'm looking for clarifications on what exactly I need to do in order to get a correct scaling of 1-4 interactions for OPLS-AA in a topology made by x2top. Specifically, will the command x2top -f in.gro -o out.top result in a topology that, when fed into grompp, will give a .tpr

Re: [gmx-users] Is Gromacs CUDA compatible

Hi, Just came across this page: https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600 - you might want to check it out :) 2009/2/5 Jagdish S. Varma > Hello, > > Can anybody help me. I need to check if Gromacs is CUDA compatible. If not, > is there any other middle-ware that wi

Re: [gmx-users] Software for ESP fitting

2008/9/8 David van der Spoel <[EMAIL PROTECTED]> > Vasilii Artyukhov wrote: > >> Hi gmx-users, >> >> Sorry for a not-strictly-GROMACS-related question, but could someone >> suggest a program I could use to fit atomic charges to quantum chemistry >> r

[gmx-users] Software for ESP fitting

Hi gmx-users, Sorry for a not-strictly-GROMACS-related question, but could someone suggest a program I could use to fit atomic charges to quantum chemistry results? Thanks in advance, Vasilii ___ gmx-users mailing listgmx-users@gromacs.org http://ww

[gmx-users] Velocity ACF not decaying to zero

Dear all, I'm trying to compare the diffusion constants resulting from g_msd -mol and g_velacc -mol -nonormalize. The agreement for pure water (512 molecules, 300 K) seems fine (g_analyze output of g_velacc falls into the +- interval of g_msd), but for a more complex system (4000 waters + 80 small

Re: [gmx-users] Re: g_rdf: normalization issues?

08 15:18:47 +0400 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: g_rdf: normalization issues? > > > Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the > molecule); still, the integrated RDF values seem to deviate from wh

[gmx-users] Re: g_rdf: normalization issues?

Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the molecule); still, the integrated RDF values seem to deviate from what ithey're supposed to be... 2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>: > Hi, > > I'm using g_rdf 3.3.3 to analyze th

[gmx-users] g_rdf: normalization issues?

Hi, I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in water. What puzzles me is that sometimes in, e.g., two sequential runs, I get two RDF's with one of them having *uniformly* larger values than the other. Given the fact that the RDF should in principle be normalized, thi

Re: [gmx-users] force field parameters for hydronium

http://www.rsc.org/Publishing/Journals/DT/article.asp?doi=b516258k 2008/4/28 David van der Spoel <[EMAIL PROTECTED]>: > Vasilii Artyukhov wrote: > > > > > 2008/4/28 Mark Abraham <[EMAIL PROTECTED] > [EMAIL PROTECTED]>>: > > > > > > Trying t

Re: [gmx-users] force field parameters for hydronium

2008/4/28 Mark Abraham <[EMAIL PROTECTED]>: > Trying to model hydronium is a pretty flawed thing to do, since the > hydrogens in real water are labile - so the molecule you'd label as > "hydronium" moves much faster than any atoms do. I actually seem to remember reading something about some dis

Re: [gmx-users] Need help with installation on Itanium2

Yep, my mistake, I built the serial version using gcc previously, so the problem really _is_ in Intel's compiler. I've finally figured out how to make mpicc use gcc instead of Intel, so now I have a working MPI version of GROMACS. Thank you again, Vasilii 2008/4/28 Mark Abraham <[EMAIL PROTECTED]

Re: [gmx-users] Need help with installation on Itanium2

Thanks for quick reply, 2008/4/28 Mark Abraham <[EMAIL PROTECTED]>: > Vasilii Artyukhov wrote: > > > Dear everyone, > > > > I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a > > certain point, the compilation crashes with > >

[gmx-users] Need help with installation on Itanium2

Dear everyone, I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a certain point, the compilation crashes with */bin/sh ../../../../libtool --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/X11R6/include -I../../../../include -DGMXLIBDIR=\"/nethome/dvasya/6

Re: [gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

Thanks Chris and Mark! 2008/4/21 Chris Neale <[EMAIL PROTECTED]>: > I use tip4p/opls/berger combination and it works well for me. I have never > used tip5p. I suggest that you build your membrane and run one control > simulation (sounds like you would lean toward using spc for this) and then > on

[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

Dear GROMACS users, particularly, those experienced with membrane simulations, I want to simulate lipid bilayers (e.g., DPPC) in the presence of certain small solutes, much like what was done in A.K. Sum & J.J. de Pablo, Biophys. J. 85, 3636 (2003) with DMSO. I'd like to use the TIP5P and OPLS al

Re: [gmx-users] water can't freeze

Dear Xiupeng, What you're seeing is the difference between freezing water and overcooling it. If you want your water to crystallize, you'll actually have to make it - e.g., by putting it in contact with ice. Normally, pure water doesn't freeze on its own, you can easily verify this experimentally

Re: [gmx-users] CPMD and gmx

Dear Andrey, The maximum time step depends on whether you're doing Born-Oppenheimer or Car-Parrinello MD. In the case of usual BO MD, you normally want a time step of 0.5-1.0 fs, possibly 2 fs, if you use rigid molecules. In the CP case, you have to use a much smaller time step to make sure that t

Re: [gmx-users] POL3 polarizable water model

I believe the manual says that only the shell-on-a-spring model is supported by GROMACS for polarization. As far as I can recall, the POL3 model uses atomic multipoles, so tough luck for you... 2008/3/25, Bo Zhou <[EMAIL PROTECTED]>: > > Dear Gromacs users, > > I wonder whether or not the POL3 pol

Re: [gmx-users] g_rdf -[no]com

Ok, thanks! 2008/1/11, Berk Hess <[EMAIL PROTECTED]>: > > > > > > > Date: Fri, 11 Jan 2008 15:58:23 +0100 > > From: [EMAIL PROTECTED] > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] g_rdf -[no]com > > > > Oh yes, the -rdf option! And the run input file!

Re: [gmx-users] g_rdf -[no]com

he COM of the molecule and water oxygen (which is I suppose what I request it to produce). However, using -rdf mol_com seems to work fine. 2008/1/11, David van der Spoel <[EMAIL PROTECTED]>: > > Vasilii Artyukhov wrote: > > Hi everybody, > > > > I'm dealing wi

[gmx-users] g_rdf -[no]com

Hi everybody, I'm dealing with aqueous solutions of some small molecules. Just to clarify: 1) When I type g_rdf, is the -com option on by default? g_rdf -h makes me suspect it is... 2) When I type g_rdf -nocom, what point of the molecule does the resulting RDF correspond to? 3) g_rdf -h says that

Re: [gmx-users] Gromacs-MPI cygwin

Just a thought... Maybe you should instead try WMPI (or whatever the thing is called, you know, MPI for Windows...) and some of the Windows ports of GROMACS that you can find in the user contributions area of the website. That's supposing you really _need_ to use MPI, of course :) In my case, thou

[gmx-users] GROMACS and GPU (and PS3)

Hi everybody, I wonder if GROMACS will eventually support running on the graphics cards, especially since there have been several announcements of extremely powerful cards like AMD's FireStream recently. I know that the question has repeatedly been asked some time ago, but hey, the Stanford guys f

Re: [gmx-users] fullerene topology

2007/12/5, Adam Fraser <[EMAIL PROTECTED]>: > > > I just need accurate partial charges to build the topology file with. Well, if you really meant what your message said, the answer should be exactly 0.0 a.u. on every atom. ___ gmx-users mailing list

Re: [gmx-users] GROMACS in parallel on a multicore PC?

Thanks for the quick response :) 2007/11/21, Carsten Kutzner <[EMAIL PROTECTED] >: > > Hi Vasilii, > > > > - Does GROMACS support multithreaded execution & how efficient is it? > As far as I know this is planned, but not supported yet. Ok, but what about the underlying math libs? Would using threa

[gmx-users] GROMACS in parallel on a multicore PC?

Hi everybody, Sorry for a somewhat technical question, but I'd like to know which is the best way to run GROMACS on a SMP machine (in particular, a multicore PC). The (known) points of interest are: - Does GROMACS support multithreaded execution & how efficient is it? - Should I rather use some

Re: [gmx-users] queue up simulations

Hi, I think what you're looking for is called a shell script :) 26 Oct 2007 06:01:31 -, sarbani chattopadhyay < [EMAIL PROTECTED]>: > > hi, > > I want to know is there any way to 'queue up mdrun jobs' so that once > one job is > finished, the next starts automaticaly? > > Thanks in adva

Re: [gmx-users] Rerefence on Berendsen vs. Nose-Hoover

There's a reference in the manual, where the T-coupling schemes are first introduced. 2007/10/15, Jochen Hub <[EMAIL PROTECTED]>: > > Hi, > > I think there is a paper around which says that for parcticle purposes > it hardly matters whether one uses Berendsen or Nose-Hoover T-coupling. > Does anyo

Re: [gmx-users] Help for simulating the metalcluster

Sorry for advertising a competitor code on the list :) but you might want to check out the DL_POLY package, as well... 2007/10/1, Utpal Sarkar <[EMAIL PROTECTED]>: > > Dear Gromacs Users, >I want to use GROMACS code to simulate the metal cluster > (say Iron or Na) on > substrate (s

Re: [gmx-users] Troubles with genbox and random insertion

That's the whole idea, you _have_ to change the seed value, since it's used by the program to generate a sequence of pseudorandom numbers... 2007/9/18, Shay Amram <[EMAIL PROTECTED]>: > > Greetings Ran, > > I tried to add the –seed flag as you said, at the end of each genbox (with > different vari