[gmx-users] mdrun cannot append to file larger than 2Gb

nt in compiling that has left mdrun a little broken? Thanks, Warren Gallin-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post

[gmx-users] Input files for g_bar

? Warren Gallin-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or

[gmx-users] Help with using g_bar

. Could someone suggest where I am going wrong, and even better where I might find some documentation of the operational use of g_bar? Thanks, Warren Gallin Long-to-short dhdl file.pdf Description: Adobe PDF document Short-to-long dhdl file.pdf Description: Adobe PDF document

Re: [gmx-users] Help with using g_bar

On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote: > > > Warren Gallin wrote: >> I am trying to use g_bar to derive a PMF curve from non-equilibrium >> trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7. >> I am using the end-to-end distance of a pe

[gmx-users] Question about g_bar output

/mole (see below). However, the graphical output from -o and -oi seem to numerically be from the kT units list, but the y-axis is labelled in kJ/mole (see atached PDF files. Am I missing something here, or is this a bug in the output code? Warren Gallin md_0.05.xvg: 0.0 - 2

Re: [gmx-users] Question about g_bar output

Justin, OK, this makes sense to me, and I can do the interconversion of units easily enough outside of the GROMACS tools. Should I file a bug report? Warren Gallin On 2011-06-29, at 12:48 PM, Justin A. Lemkul wrote: > > > Warren Gallin wrote: >> Hi, >&g

Re: [gmx-users] crazy temperatures

At that temperature most matter is going to be a plasma, not many bonds to be simulated and a lot of free electrons. Warren Gallin On 2012-03-28, at 4:43 PM, Mark Abraham wrote: > On 29/03/2012 9:39 AM, Asaf Farhi wrote: >> Dear GMCS users >> >> Hi. Does anyone kn

Re: [gmx-users] genion doesn't work in 4.6.1?

Don't you have to give tyne name of the positive and negative ions that will be added by genion? Otherwise, how would it know? Warren Gallin On 2013-04-05, at 1:05 PM, Albert wrote: > Hello: > > I found that there would be some problem of genion in 4.6.1: > > gro

[gmx-users] pdb2gmx for small molecules?

sing pdb2gmx for non-protein/nucleic acid molecules? Thanks. Warren Gallin-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don&

Re: [gmx-users] Re: Genion cannot read from input

The problem is that genion is expecting input from the command line, telling it which molecules to replace with ions - usually SOL. If you are running a script you have to script an input line for genion. Warren Gallin On 2013-04-27, at 2:56 PM, Nathan Bullock wrote: > The useful part of

Re: [gmx-users] Elastic network model

GROMACS uses nm as the unit of length, so this is 38 Angstroms, shouldn't be a problem. On 2012-08-31, at 2:23 PM, Bogdan Costescu wrote: > On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena > wrote: >> Hi all, >> I have built topology for elastic network as follows(the >> atoms

Re: [gmx-users] (no subject)

You are not specifying the ions to be added using the -pname and -nname options with the genion command. Perhaps that is a problem? Warren Gallin On 2011-07-26, at 2:49 PM, Sara baretller wrote: > thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 > -neut

Re: [gmx-users] more than 100% CPU

I believe that the current version of GROMACS supports threading, which does not require mpi. So mdrun is running threads at 100% of the activity of each of your 16 nodes, hence 1600%. Warren Gallin On 2011-08-18, at 5:19 PM, Park, Jae Hyun nmn wrote: > Hi GMX users, > > I inst

Re: [gmx-users] more than 100% CPU

It means you are running a lot of parallel processes, but that does not translate into a linear increase in speed. So faster, but not 16X. Warren Gallin On 2011-08-18, at 5:36 PM, Park, Jae Hyun nmn wrote: > Thank you, Warren. > Does that mean 16 times faster ? > >

[gmx-users] Designating an output directory

Hi, Is there any way to set the directory where the output from mdrun will be written if I do not want to have it in the directory from which I am giving the command? Thanks, Warren Gallin ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Unexpected Production of .pdb files

in my computer (writing intermediate data to a file?) or a known behavior of GROMACS under some conditions? Just trying to understand what's happening. Warren Gallin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

[gmx-users] Pressure swings during preliminary runs

Can someone point me at some relevant information on how to troubleshoot large rapid pressure variations? Thanks Warren Gallin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi

Re: [gmx-users] Pressure swings during preliminary runs

Justin, OK, I see what's going on. So then, since the instantaneous pressure values are so variable, is there a reason to implement pressure coupling for an MD run? Warren On 25-Aug-09, at 1:23 PM, Justin A. Lemkul wrote: Warren Gallin wrote: HI, I am trying to simulat

[gmx-users] Exploding poly-serine

rue that the high internal force present at the end of the initial energy minimization could be the root of the problem? 3) If so, is there an obvious method for relaxing the system into a more stable state prior to the main MD run? Warren Gallin ___

Re: [gmx-users] Exploding poly-serine

more susceptible to this than poly-Pro, poly- Asp or poly-Gly is not obvious to me, but I am sure that there is a reason out there somewhere. Thanks, Warren Gallin On 26-Aug-09, at 10:48 AM, David van der Spoel wrote: [Details deleted] So my questions are: 1) Am I missing some

[gmx-users] pdb2gmx problem

-- The ACE residue does not have a N atom, either in the pdb file or in ffoplsaa.hdb or in ffoplsaa.rtp, so I don't understand what the problem is. Can someone shed some light on this? Warren Gallin Gly10_Capped.pdb

[gmx-users] gmxtest failures OK?

. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 16 out of 63 kernel tests FAILED All 45 pdb2gmx tests PASSED Am I correct in thinking that these kernel failures are expected, and therefore that the installation worked? Thanks, Warren Gallin

Re: [gmx-users] gmxtest failures OK?

I could only find the 4.0.4 tests, which are what I ran. Where would I find the latest tests? Warren Gallin On 28-Aug-09, at 3:42 PM, Justin A. Lemkul wrote: Which test set are you using? These failures are to be expected for earlier versions in the 4.0.x series, but were fixed in a

Re: [gmx-users] viscosity calculation

265 K is -8C, so ice, not liquid water. That would be more viscous than you might expect. Waren Gallin On 2010-09-29, at 12:52 PM, Payman Pirzadeh wrote: > Well, two questions: > > 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like > very weird to me since experimenta

Re: [gmx-users] COM Pulling - Single Chain

code is also problematic for measuring the forces because it creates a cycle of constraints, which yields an occasional but problematic spike to huge values when trying to calculate the free energy as a function of end-to-end distance of a peptide. Warren Gallin On 2010-10-19, at 6:50 AM, chr

Re: [gmx-users] Inaccurate pressure readings

This seems odd. If a value fluctuates between -400 and +400, how can the average be outside the range? Warren Gallin On 2011-01-20, at 3:24 PM, Denny Frost wrote: > from -1000 to 1000, depending on the system. The simulation box is 8x8x8 nm > (roughly) and contains about 12,000

[gmx-users] Load balancing between PME and PP on more than 12 processors

nd the PME grid spacing are scaled by the same factor." Does this mean that cut-off and grid-spacing parameters need to be changed by the same proportion? I hope this is sufficiently specific a question - if not, let me knwo what I need to be clearer on. Thanks, Warren Gallin -- gm

[gmx-users] What is Dmax, and are .tpr files transferrable between operating systems

And second, are .tpr files platform independent, i.e. if I create a .tpr file using MacOSX, can I simply copy it onto a system running Linux invoke mdrun to run the simulation? I'm using the same version (4.0.7) on both platforms. Thanks, Warren Gallin -- gmx-users mailing list

[gmx-users] Questions about parameters

r any and all advice. Warren Gallin-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or

[gmx-users] Free energy and and-to-end distances

wondering if anyone could point me at an example of doing this kind of analysis, or else perhaps clarify how to generate the equivalent of pullx and pullf files for g_wham analysis without using the pull code. All advice gratefully accepted. Warren Gallin -- gmx-users mailing listgmx-users

[gmx-users] Constraint distance question

that the constraint is not randomly disappearing from consideration when the two ends of the peptide are in different domains. Thanks for any insights. Warren Gallin-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Constraint causing system to explode

that needs to be dealt with when imposing a type 2 constraint? Warren Gallin Step 94636, time 189.272 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.041028, max 0.161215 (between atoms 217 and 219) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous

Re: [gmx-users] Constraint causing system to explode

manifest this behavior? Warren Gallin On 2010-05-27, at 11:22 AM, chris.ne...@utoronto.ca wrote: > Dear Warren: > > I don't have your answer, but I'll point out that when you ask: "Is it > possible that this is a problem that arises because of domain decomposi

Re: [gmx-users] Constraint causing system to explode

ceed? All ideas welcome. Warren Gallin On 2010-05-31, at 10:09 PM, Mark Abraham wrote: > - Original Message - > From: Warren Gallin > Date: Tuesday, June 1, 2010 13:38 > Subject: Re: [gmx-users] Constraint causing system to explode > To: Discussion list for G

[gmx-users] Questions about g_sham

number and the smallest number by 32, and then check the expected boundary values for bin 0 and bin 31, I find lengths in the wrong bins Can anyone give me some insight into the actual workings of g_sham and what I might be doing wrong (or incorrectly expecting) here? Warren Gallin

Re: [gmx-users] Questions about g_sham

OK, what if I have only one dimension (end-to-end distance), is there any way to do that in GROMACS, or is the best way to just write a little app for myself? Warren Gallin On 2010-06-23, at 11:29 AM, Justin A. Lemkul wrote: > > > Warren Gallin wrote: >> Hi all, >>

Re: [gmx-users] Questions about g_sham

wrote: > Warren Gallin wrote: >> OK, what if I have only one dimension (end-to-end distance), is there any >> way to do that in GROMACS, or is the best way to just write a little app for >> myself? > > Sounds to me like a problem for PMF, but I seem to recall you had s