[gmx-users] segemntation fault after run do_dssp

Hi All, I already done the MD production so I want to analyse the helical structure of my protein by using do_dssp program.The command is like below : do_dssp -s md_water50.tpr -f md_water50.trr -n mainchain.ndx -sc dssp_scount.xvg -a dssp_area.xvg -ta dssp_totarea.xvg -aa dssp_averarea.xvg but

[gmx-users] energ minimization: cg and I-bfgs

Hi, protein have 2 positive chage, I use PRODRG built .gro of CH3C00H, and add two molecular CH3C00H, four molecular NA into system. At energy minimization step, after steep, when I use cg, Fatal error: DD cell 1 4 0 could only obtain 14 of the 16 atoms that are connected via constraints from the

[gmx-users] Regarding mdrun

Dear gmx-users, I am experiencing some strange things while performing mdrun. I am running a CG simulation and it is terminating with LINCS warnings after approx. 500ns of simulation. If I restart it with the check point file, then its running with out any errors. Is my simulation is reliable?? I a

[gmx-users] Unable to download Gromacs source tar file

Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by Mail

Re: [gmx-users] mdrun segmentation fault for new build of gromacs 4.6.1

Hi, I recommend to run the regressiontests. The simplest way is to build GROMACS with cmake -DREGRESSIONTEST_DOWNLOAD, and run make check. See http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.12._Testing_GROMACS_for_correctness for more details. Roland On Thu, Jun 6, 2013

RE: [gmx-users] Is non-linear data output/storage possible?

Easiest, naïve way that I can see is to do the simulation in blocks, and change the output settings within the mdp file used as required for each block. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville V

Re: [gmx-users] xx of the xxxx bonded interactions couldn't be calculated

On 6/6/13 10:00 PM, Badamkhatan wrote: Dear GMX-users Recently i got this error and note from my MD2 simulation. I'm solvating 1-octanol to 1-octanol and calculating free energy differences. This is the last step of my calculation and previous steps are looking fine. Basically i followed Justi

[gmx-users] xx of the xxxx bonded interactions couldn't be calculated

Dear GMX-users Recently i got this error and note from my MD2 simulation. I'm solvating 1-octanol to 1-octanol and calculating free energy differences. This is the last step of my calculation and previous steps are looking fine. Basically i followed Justin's free energy tutorial. Here is Note:

[gmx-users] Re: cg Fatal error--DD cell

the information on .log as follows: Initializing Domain Decomposition on 2 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.598 nm, LJ-14, atoms 942 950 multi-body bon

[gmx-users] mdrun segmentation fault for new build of gromacs 4.6.1

Gromacs users: I have just built and installed gromacs-4.6.1 on my Xeon 5500 compute cluster running Centos 5. The installation was done with gcc 4.7.0 I have run a simple test (the old tutor/gmxdemo) which fails at the first mdrun step with a segmentation fault. The command line for this ste

Re: [gmx-users] No default Ryckaert-Bell. types

On 6/6/13 11:52 AM, Nilesh Dhumal wrote: I checked the line number in .top file. Its not reading any dihedral parameter defined in .itp file. Well, if it's not reading parameters, then that explains the error that tells you there are no parameters defined. -Justin On 6/6/13 9:22 AM, Nil

Re: [gmx-users] No default Ryckaert-Bell. types

I checked the line number in .top file. Its not reading any dihedral parameter defined in .itp file. NIlesh > > On 6/6/13 9:22 AM, Nilesh Dhumal wrote: >> Hello, >> >> I am getting "No default Ryckaert-Bell. types" error for grompp. >> >> I have define all this parameter in .itp file >> >> Here i

Re: [gmx-users] No default Ryckaert-Bell. types

On 6/6/13 9:22 AM, Nilesh Dhumal wrote: Hello, I am getting "No default Ryckaert-Bell. types" error for grompp. I have define all this parameter in .itp file Here is .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ de

Re: [gmx-users] Re: pullx file content with pull_geometry = position

On 6/6/13 5:17 AM, Bastien Loubet wrote: I update the post to say that we tried to make a rerun of the trajectory on our local machine and the output of the pullx.xvg file (created with the option -px of mdrun) is: # This file was created Wed Ju

Re: [gmx-users] Segmentation fault (core dumped)

On 6/6/13 4:45 AM, Ishwor Poudyal wrote: Dear all I want to study the diffusion coeffcient of CO in water. I have done the energy minimization step and got the problem segmentation fault during Equilibration. I am confused whether my input file has got some error or the err

[gmx-users] Getting .edr file data as a generic data file

Hi again! At the moment, the only way I know how to access .edr files is through the use of g_energy. However g_energy only outputs .xvg files which is fine for routine analysis. However if I want to get into further processing, it would be helpful if I could get the information stored in the .edr

Re: [gmx-users] Eigenvector and eigenvalues

Hi Ankita, Please provide the commands you've run and the screen output from g_covar. Cheers, Tsjerk On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani wrote: > Hi, > > I wanted to know about the eigenvectors and eigenvalues. I recently > performed the principal component analysis (only the bac

[gmx-users] Eigenvector and eigenvalues

Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed the principal component analysis (only the backbone into consideration) on a trajectory of 2000 residues. I obtained 15641 eigenvectors and 17928 eigenvalues. There is a difference in the number, which I am not quite

[gmx-users] No default Ryckaert-Bell. types

Hello, I am getting "No default Ryckaert-Bell. types" error for grompp. I have define all this parameter in .itp file Here is .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ defaults ] ; nbfunccomb-rule gen

[gmx-users] cg Fatal error--DD cell

1)I use steepest to minimize energy, .mdp as follows, title = bovin cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps

[gmx-users] Is non-linear data output/storage possible?

Hi everybody! This is a sort-of general question that I am not sure where to find the answer for. I am running a simulation on the order of tens of microseconds. However I also want to do some analysis on the order of very small time steps but I do not want to save the data of very small time step

Re: [gmx-users] Projection of crystal structure on PCA plot

Thanks a lot Tsjerk :) -Anirban On Thu, Jun 6, 2013 at 4:42 PM, Tsjerk Wassenaar wrote: > Hi Anirban, > > Indeed. > > :) > > Tsjerk > > > On Thu, Jun 6, 2013 at 1:11 PM, Anirban >wrote: > > > Dear Tsjerk, > > > > Thank you very much for the explanation. > > > > So, in other words, as I have ca

Re: [gmx-users] Projection of crystal structure on PCA plot

Hi Anirban, Indeed. :) Tsjerk On Thu, Jun 6, 2013 at 1:11 PM, Anirban wrote: > Dear Tsjerk, > > Thank you very much for the explanation. > > So, in other words, as I have carried out PCA on the basis of CA atoms from > the MD trajectory, so if I wish to project the crystal structure onto the

Re: [gmx-users] Projection of crystal structure on PCA plot

Dear Tsjerk, Thank you very much for the explanation. So, in other words, as I have carried out PCA on the basis of CA atoms from the MD trajectory, so if I wish to project the crystal structure onto the EV, then I need to consider only the CA atoms of the crystal structure (which in that case wo

Re: [gmx-users] Projection of crystal structure on PCA plot

Hi Anirban, The eigenvectors obtained from the simulation are a way of rewriting the coordinates of your structures, not in terms of atoms-XYZ, but as combinations of these. Because they are combinations of atom-positions, they are defined for the selection of atoms used for the calculation. If yo

Re: [gmx-users] Snapshot and co-ordinate query

Hi Justin, Thank you so much for the clarification. Kind regards, Ankita On Wed, Jun 5, 2013 at 11:28 PM, Justin Lemkul wrote: > > > On 6/5/13 3:03 PM, Ankita naithani wrote: > >> Hi, >> >> I have two questions. >> >> I have performed a simulation on my protein structure and after the >> si

[gmx-users] Projection of crystal structure on PCA plot

Hi ALL, I have carried out a simulation of a protein and have carried out PCA on the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2. Now I want to locate the conformation of the crystal structure (with which I started the MD) on this map. How to do this? Can I use "g_anaeig

[gmx-users] Re: pullx file content with pull_geometry = position

I update the post to say that we tried to make a rerun of the trajectory on our local machine and the output of the pullx.xvg file (created with the option -px of mdrun) is: # This file was created Wed Jun 5 12:15:49 2013 # by the following command

[gmx-users] Segmentation fault (core dumped)

Dear all I want to study the diffusion coeffcient of CO in water. I have done the energy minimization step and got the problem segmentation fault during Equilibration. I am confused whether my input file has got some error or the error is in the processing machine.I have made