Re: [gmx-users] g_wham error analysis hangs

errors. > > If this error still occurs with the latest version, could you make a > tar-ball of your tpr and pullf files, put them online, and send me the link? > > Then I will try to fix the bug. > > Best, > Jochen > > > Am 8/5/13 8:29 AM, schrieb Magnus Ander

Re: [gmx-users] g_wham error analysis hangs

> What version of Gromacs are you using? How many data points do you have in > the full set? > > -Justin > Gromacs 4.6 not sure what you mean by data points, but: dt = 0.002 nsteps = 100 and total number of atoms in the system: 265,891 # frames

Re: [gmx-users] g_wham error analysis hangs

> > I've had this happen before when trying to analyze too many data points. Try > reducing the size of the input data using -b to see if that helps. > > -Justin Thanks for the suggestion, Justin. However, either it hangs or I get: Fatal error: Tryig to estimtate autocorrelation time from on

[gmx-users] g_wham error analysis hangs

Hi, I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do: g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 50 -bins 50 -bs-method traj-gauss -bsres -ac y

[gmx-users] GROMOS 53A6 AND charmm36.ff

he charmm36.ff forcefield? Best regards / Magnus Andersson ======= Magnus Andersson, PhD Department of Physiology and Biophysics University of California, Irvine Irvine, CA 92697-4560 (949) 824-6993 Fax: (949) 824-8540 === -- gmx-

[gmx-users] membranes & proteins revisited

run: genbox -cp protein.gro -cs membrane.gro if I just run it as it is, I get: Checking Protein-Solvent overlap: tested 1512 pairs, removed 9261 atoms. I feel I'm getting there, but need some advice to come to the point where I have my trimer in a "relaxed" membrane... Thanks /

[gmx-users] insert protein in membrane again

Hi again, As I use genbox with my .gro file holding the protein and my .gro file containing the membrane I get the error message: Fatal error: Invalid line in protein.gro for atom 2296: There is no atom 2296 in protein.gro... I must be missing something? /Magnus -- Magnus Andersson

[gmx-users] insert protein in membrane

otein .top file and the membrane .gro file I already have. (I have tried generating a .top file from the membrane .gro file (pdb2gmx), doesn't work. It deletes "duplicate atoms". Can someone give me step-by-step instructions to this problem. Greatly appreciate your help! /Magn

[gmx-users] segmentation fault

RNING relative constraint deviation after LINCS: max 0.001312 (between atoms 2265 and 2266) rms 0.51 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2262 2263 30.00.1089 0 Thankful for a reply / Magnus Ande

[gmx-users] atomic mass

HI, If I want to change atomic mass of an ion, should I change ff.atp or ions.itp? /Magnus ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. U

[gmx-users] tbpconv

Hi, I used tbpconv to restart a crashed run. This will result in 2 separate .xtc and .trr files. How can I use for instance g_rdf on these files. Is there some way to fuse them? /Magnus Andersson ___ gmx-users mailing listgmx-users@gromacs.org