[gmx-users] regarding energy run and g_lie

בתאריך 15 בספטמבר 2011 12:58, מאת גדעון לפידות : > Hello GMX users, > > I have a couple of questions regrading energy run and g_lie: > 1. I am interested in calculating the estimated binding energy between pip2 > and a protein using the lie method. > 2. I have run the protein l

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 83

Hello GMX users, I have a couple of questions regrading energy run and g_lie: 1. I am interested in calculating the estimated binding energy between pip2 and a protein using the lie method. 2. I have run the protein ligand complex for 40 ns with counter-ions, npt ensemble and PME 3. In order to c

[gmx-users] g_lie (again..)

Hi all, Could anyone please refer to me to a paper or other resource that explains in detail (specifically technical) on how to preform g_lie. I know the matter has been brought up here quit often lately but looking through the mailing list archives and reference papaers (Aquist et al. and similar

[gmx-users] Re: g_covar

Thanks for your replies. I would like to clarify regarding my first questionn. I don't want a g_dist matrix. I would like to get a covariance matrix where the values correspond to absolute distance and not dived into different dimensions. for example say I have a protein with 100 aa and I run g_cov

[gmx-users] g_covar

Hi all, I have a couple of questions regarding g_covar: First, is there anyway to specify that the covar.dat output will be in R distance (meaning sqrt(x^2+y^2+Z^2)) and not in separate Cartesian coordinates? also when examining the output I don't understand how the main diagonal values are differ

[gmx-users] compiling 4.0.7 md run to Gromacs 4.5.3

Hi all, I was wondering if there is any way to take an MDrun done on Gromacs 4.0.7 and converting it so it is compatible with Gromacs 4.5.4. Best, Gideon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

[gmx-users] Protein ligand segmentation fault

Hi all, I have been trying to run a protein ligand simulation in water using Gromacs version 4.0.7 and GROMOS 53a6 ff. My protein is about 250 aa and my ligand is pip3 (Phosphatidylinositol (3,4,5)-trisphosphate) which I have constructed using PRODRG (using EM and full charges option). I have tried

[gmx-users] different RMSD graphs after using pbc mol

Hi all, I was wandering if anyone knows of a problem with gromacs 4.0.7 when it comes to its RMSD tool. After running a 44 ns simulations on a soluble protein I used g_rms to calculate RMSD . The results did not seem to make sense ( >30 angstrom at some time points). After running pbc-mol and cent

[gmx-users] ion jumping out of water box

Hi all, I have been running simulations of a soluble protein bound to a pair of calcium ions. I have been running this simulation in 4 nano second intervals. everything looks fine until the 14th nano second when one of the ions just jumps out of the water box. pbc-mol does not correct the problem.

[gmx-users] MPIRUN on Ubontu

Hi all, I have recently installed Ubonto on my computer (i5 processor) and installed gromacs 4.0.7. I have installed openmpi and fftw but when using mpirun command instead of getting parallel processes it simply runs the same job four times simultaneously. How do I make the necessary adjustments. T

[gmx-users] Calculate ion disasociation constant

Hi all, Does anyone know of way I can use Gromacs to calculate the disasociation constant of a calcium ion held by two loops in a protein in water simulation? my starting point was a pdb file of the protein with the bound ions in place. Eventually I would like to evaluate the time constant (meaning

[gmx-users] Protein jumping out of water box

Hi all, I have been running nano second long simulations using Gromacs 4.0.7 and connecting them to create a long time period. on the last run the protein "jumped" out of the water box (the output files were viewed using VMD) does anyone know why this could have happened? Thanks, Gideon -- gmx-use

[gmx-users] VDW radious (Gideon)

Hi all, General question, what is the significance of the VDW radious in the mdp files? for instance switching from 1.0 to 1.2, Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppor

[gmx-users] Claculating Equilibrium constants

Hello all, I have a protein bound to ions. is there a way to calculate the Kd of the bound ion in Gromaces so I can compare it to experimental Kd? Thanks, Gideon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt