Re: [gmx-users] Re: System size and minimum image convention

2013-02-22 Thread Elisabeth
Hi Vitaly, When you say interaction site you mean number of atoms in the box? How one can obtain the interaction sites? Thanks On 22 February 2013 05:04, Dr. Vitaly Chaban wrote: > >why for a binary > > (solute+solvent) the size should be larger than 2 Rc? I thought minimum > > image conventio

Re: [gmx-users] Is gromacs4.6 incompatible with some old tpr files?

2013-02-22 Thread David van der Spoel
On 2013-02-23 06:06, Daniel Wang wrote: > Hi guys~ > I have a tpr file which works perfectly with gromacs4.5. When using > gromacs4.6 with only 1 mpi process, it works normally. However, something > went wrong when process number came to 2 or more. > > e.g. > mpirun -n 6 mdrun_mpi -s gmx_workload2

[gmx-users] Is gromacs4.6 incompatible with some old tpr files?

2013-02-22 Thread Daniel Wang
Hi guys~ I have a tpr file which works perfectly with gromacs4.5. When using gromacs4.6 with only 1 mpi process, it works normally. However, something went wrong when process number came to 2 or more. e.g. mpirun -n 6 mdrun_mpi -s gmx_workload2.tpr then it crashes: Reading file gmx_workload2.tpr

Re: [gmx-users] Gromacs 4.6 Installation under Cygwin

2013-02-22 Thread Mirco Wahab
On 23.02.2013 01:59, toma0...@umn.edu wrote: Hello, I am trying to install Gromacs 4.6 on a Windows workstation under cygwin. After I install everything, when executing g_luck I come up with the error: 'error while loading shared libraries: cyggmx-6.dll: cannot open shared object file: No su

[gmx-users] Gromacs 4.6 Installation under Cygwin

2013-02-22 Thread toma0052
Hello, I am trying to install Gromacs 4.6 on a Windows workstation under cygwin. After I install everything, when executing g_luck I come up with the error: 'error while loading shared libraries: cyggmx-6.dll: cannot open shared object file: No such file or directory' There does exist t

[gmx-users] g_chi and J coupling

2013-02-22 Thread Tomek Wlodarski
Hi, I wanted to check how I can calculate J couplings with gromacs. And as a test I have choosen NMR ensemble of ubiquitin from this paper: "Simultaneous determination of protein structure and dynamics" Lindorff-Larsen, Nature2005 I used g_chi: g_chi -f 1XQQ.pdb -s 1XQQ.gro -g And I always end u

Re: [gmx-users] position restrain of DNA

2013-02-22 Thread Justin Lemkul
On 2/22/13 4:37 AM, Mehdi Bagherpour wrote: Tanks Justin Should I use from 'define = -DPOSRES' in mdp file? Use whatever #ifdef construct makes sense. The -DPOSRES uses the default posre.itp written by pdb2gmx, which restrains all heavy atoms. Unless you've modified the topology, that

Re: [gmx-users] Energy minimization

2013-02-22 Thread Justin Lemkul
On 2/21/13 9:10 PM, Kieu Thu Nguyen wrote: Dear all, I can not distinguish when the Fmax < 10 kJmol-1nm-1, < 100, < 1000 ? is appropriate Can anyone tell me which value is appropriate for lipid membrane, for protein in water, for protein in lipid membrane ? There is no absolute rule. Th

[gmx-users] g_energy -nbmin -nbmax options

2013-02-22 Thread Juliette N.
Hi everyone, I am trying to calculate error of total energy in edr file using -nbmin -nbmax options. -nbmax 5 is giving 3% error while -nbmax 3000 gives an error of 0.91. Can one arbitrarily pick a large -nbmax to obtain less error? g_energy -f*.edr -nmol X -b XXX -o -nbmin 5 -nbmax 5 Energy

Re: [gmx-users] trjconv woes (broken molecules)

2013-02-22 Thread Ignacio Fernández Galván
--- On Tue, 19/2/13, Justin Lemkul wrote: > First use: > > trjconv -trans x y z -pbc mol > > This will allow you to reposition the elements of your > system such that you have an intact structure at the > origin. Then use the structure created as your new > reference structure for further trjc

[gmx-users] regarding the cosine content analysis

2013-02-22 Thread Ahmet yıldırım
Dear users, I performed MD simulation of 400 ns of a structure. I used the cosine content to check whether the simulation is not converged. I used last 100 and 50 ns of trajectory to the analysis, respectively. The results were very similar to each other.The cosine contents of the first ten princi

Re: [gmx-users] Distance for window spacing in US?

2013-02-22 Thread Andrei Neamtu
Hi, As i understand, if pulling geometry is set to 'pull_geometry = distance' and 'pull_dim = Y Y Y" then the DISTANCE between the COM of the enzyme and the ligand is restrained with the umbrella potential. If using long enough simulation times for each restraint umbrella window, as long as the li

Re: [gmx-users] position restrain of DNA

2013-02-22 Thread Mehdi Bagherpour
Tanks Justin Should I use from 'define = -DPOSRES' in mdp file? On Fri, Feb 22, 2013 at 4:13 AM, Justin Lemkul wrote: > > > On 2/21/13 7:35 PM, Mehdi Bagherpour wrote: > >> Thanks Justin >> >> I have any question? >> >> i will use minimization with this restrain. >> >> using genrestr I make m

Re: [gmx-users] order in index and matrix

2013-02-22 Thread Erik Marklund
Hi, Search the mailing list archives. This is admittedly confusing and has been discussed several times. Best, Erik On Feb 22, 2013, at 7:30 AM, Kavyashree M wrote: Dear users, I just wanted a small clarification whether the order of elements in matrix (-hbm) corresponds to reverse orde

Re: [gmx-users] Distance for window spacing in US?

2013-02-22 Thread Erik Marklund
On Feb 22, 2013, at 1:13 AM, Justin Lemkul wrote: On 2/21/13 6:24 PM, Yun Shi wrote: So in umbrella sampling, does it really matter if the vector connecting the COMs of protein and ligand is NOT parallel with the vector of the pulling force (although the pull rate is 0)? I guess as long as t