[gmx-users] Removing water from a trajectory
Hi ALL, I have a system consisting of protein+lipid+ligand+water which has been simulated for 10 ns. Now I want to make a compressed trajectory from the original one by keeping only the protein and the ligand. I am trying to do so by using trjconv with an index file. But every time trjconv is showing the default options and I am not able to select the protein and the ligand simultaneously to generate the output. How can I do this? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Removing water from a trajectory
On 14/07/2010 4:54 PM, Anirban Ghosh wrote: Hi ALL, I have a system consisting of protein+lipid+ligand+water which has been simulated for 10 ns. Now I want to make a compressed trajectory from the original one by keeping only the protein and the ligand. I am trying to do so by using trjconv with an index file. But every time trjconv is showing the default options and I am not able to select the protein and the ligand simultaneously to generate the output. How can I do this? You need to make an index file with a suitable group, and supply that to trjconv with -n, rather than relying on the auto-generated defaults. See http://www.gromacs.org/Documentation/File_Formats/Index_File and its links. Mark -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Removing water from a trajectory
You should include -n at the end of you trjconv command-line. This tells trjconv to show options from index.ndx. Regards, -Shay Quoting Anirban Ghosh reach.anirban.gh...@gmail.com: Hi ALL, I have a system consisting of protein+lipid+ligand+water which has been simulated for 10 ns. Now I want to make a compressed trajectory from the original one by keeping only the protein and the ligand. I am trying to do so by using trjconv with an index file. But every time trjconv is showing the default options and I am not able to select the protein and the ligand simultaneously to generate the output. How can I do this? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_cluster Jarvis-Patrick
Hi, The nearest neighbours are defined according to RMSD between the structures. If M=10, a new conformation x is added to a given cluster when a conformation y in the cluster exists such that: (1) x and y are neighbours, i.e., x has y among the 10 conformations with minimal RMSD to x and vice versa for y. (2) x any y have at least P (default: 3) neighbours in common. You may want to prepare a diagram to graphically illustrate this. Ran Marc Charendoff wrote: Hello, In the Jarvis-Patrick method g_cluster shows that when M=0, the cutoff is used to determine nearest neighbors (those within X.X nm). In the absence of cutoff - e.g. M is defaulted to 10, how are nearest neighbors determined? What does M=10 (or anyother number) mean? Thanks, Marc -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] version 4 pdb2gmx with ffamber broken on Mac?
While trying to get the gro and topology on a Mac using GMX v. 4.0.5 or 4.0.7, I get from running pdb2gmx -f myfile.pdb -ff amber03 -ignh WARNING: atom H is missing in residue ALA 2 in the pdb file You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual) This effect appears even after tricks like deleting ALA 2, putting an H atom in manually, among other things. Things that work: 1. Same command works on Linux using GMX 4.0.5 2. Same command works on Mac using GMX 3.3.1 3. Same command works if I use OPLS/AA-L rather than ffamber03 To reiterate, things that don't work: 1. Command gives the above WARNING on Mac using GMX 4.0.5 and 4.0.7 2. Command gives the above WARNING on Mac using GMX 4.0.5 using ffamber99sb I did not test any other platforms or force fields. Please let me know if contacting the Master and Commander of ffamber directly rather than bothering you folks. Thanks, Dan -- Tu ne cede malis, sed contra audentior ito. -- Virgil -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] version 4 pdb2gmx with ffamber broken on Mac?
Daniel Ensign wrote: While trying to get the gro and topology on a Mac using GMX v. 4.0.5 or 4.0.7, I get from running pdb2gmx -f myfile.pdb -ff amber03 -ignh WARNING: atom H is missing in residue ALA 2 in the pdb file You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual) This effect appears even after tricks like deleting ALA 2, putting an H atom in manually, among other things. Things that work: 1. Same command works on Linux using GMX 4.0.5 2. Same command works on Mac using GMX 3.3.1 3. Same command works if I use OPLS/AA-L rather than ffamber03 To reiterate, things that don't work: 1. Command gives the above WARNING on Mac using GMX 4.0.5 and 4.0.7 2. Command gives the above WARNING on Mac using GMX 4.0.5 using ffamber99sb I did not test any other platforms or force fields. Please let me know if contacting the Master and Commander of ffamber directly rather than bothering you folks. Are you using the correct nomenclature for the terminal residues? I know I've seen this happen if the first residue is not appropriately named NXXX. Point #2 below: http://ffamber.cnsm.csulb.edu/#usage -Justin Thanks, Dan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] version 4 pdb2gmx with ffamber broken on Mac?
Justin wrote: Are you using the correct nomenclature for the terminal residues? I know I've seen this happen if the first residue is not appropriately named NXXX. Point #2 below: http://ffamber.cnsm.csulb.edu/#usage -Justin No, I've got the right residue nomenclature. The problem was that I was using the wrong aminoacids.dat. We're using a modified version of ffamber03, and a peculiar dolt (me) neglected to fully install the ffamberXX files ... like the modified aminoacids.dat. Thanks, Dan -- Tu ne cede malis, sed contra audentior ito. -- Virgil -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] NPT for compressing the system
Hello, Thanks for your reply. As for the simulation box, I did not change anything and I am still saying that I am having a cubic box of size 30nm. When I view the molecule in ngmx I see the cubic box.. no problem with that. What I was referring to was the option on menu bar where one can select type of box to view the trajecotry and using say triclinic box I see chain fits better (almost completely)in the box while in the case of cubic (which is my real box) I see molecules is not fitted completely inside the box.. I was just asking why is this happening. as you said none of that probably means anything . I think also it is unnecessary for now so please dont get confused. As you requested I am including ALL the commands I used from the very beginning starting from replicating a 4C unit. editconf -f Eth4C.pdb -o Eth4C-d.gro -princ -d 0.058 -bt cubic editconf -f Eth4C-d.gro -o Eth4C-d-index.gro -n index.ndx -princ genconf -f Eth4C-d-index.gro -o Eth4C-d-index-rep30.gro -nbox 30 1 1 now I have PE chain of 60 units. using proper rtp and hdb files: pdb2gmx -f Eth4C-d-index-rep30-res.gro -o Eth4C-d-index-rep30-res-pdb2.gro -p Eth4C-d-index-rep30-res-pdb2.top -ff oplsaa output.pdb2gmx Then I EM this last gro file but since dimensions are 15 * 0.5 0.5 nm I am getting the error message : The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. then increased the size editconf -f Eth4C-d-index-rep30-res-pdb2.gro -o Eth4C-d-index-rep30-res-pdb2-boxsize30.gro -box 30 30 30 -angles 90 90 90 Then I EM the molecule with new box size 30nm and call this energy minimized structure PE60.gro. Now I want to replicate this chain. density demands 1 molecule in 5.76 nm3. As you said I forgot the density for a moment and took a large box. PE60 is already in a large enough box (30nm). this is all I did before doing any NPT. As for compressing the system to get more realistic structure and approaching the density I am after, I did several NPT runs. All show system is not equilbrated and they all crash and box does not become smaller than 2.2 nm. As you proposed I tried doing runs in stepwise manner. Below you see my trails: First trial :P 120 bar for 100 ps then P80 bar for 500 ps then P50 for 500 ps. this last run crashes at 2.2 nm size As Mark suggested I tried started with lower pressure: Second trail: P 50 for 500ps P40 bar for 500 ps P35 for 1000ps P30 for 1000 ps . Below is the results of this last run. before I had negative average Pressure but below the pressure is 30bar and real values fluctuate between -500 to 500 bar. T thermostat is working fine but LJ Columb terms not reaching equilibrium. Also box size is 2.7 nm which is larger than former trials.Molecule in not inside the box for almost the entire simulation.Only a small portion in inside and since it is long can not fit in. Do i need to start with lower pressures and go to higher values. Because the size is not changing that much with 30 bar? Energy Average RMSD Fluct. Drift Tot-Drift --- Angle 736.58230.054330.0543 -9.65991e-05 -0.0965993 Ryckaert-Bell. 147.60313.522613.5185 -0.00115216 -1.15216 LJ-14 153.9266.021256.02079 0.000258266 0.258266 Coulomb-14 -106.1411.909861.90613 0.00041316 0.413161 LJ (SR)-354.89215.504715.4964 -0.00176674 -1.76675 Coulomb (SR)217.5292.63621 2.6302 -0.000615852 -0.615853 Potential 794.60737.486237.4764 -0.00295993 -2.95994 Kinetic En. 899.8830.645430.6399 0.002015242.01525 Total Energy1694.4918.707118.7051 -0.000944686 -0.944688 Temperature 299.80610.209910.2081 0.000671404 0.671405 Pressure (bar) 30.0416 269.98269.948 0.014565214.5652 Cons. rmsd ()5.11735e-06 3.49122e-07 3.49102e-07 1.29073e-11 1.29073e-08 Box-X 2.79128 0.00907586 0.00906645 1.43079e-06 0.00143079 Box-Y 2.79128 0.00907586 0.00906645 1.43079e-06 0.00143079 Box-Z 2.79128 0.00907586 0.00906645 1.43079e-06 0.00143079 Density (SI)128.686 1.26011.25879 -0.000199256 -0.199256 pV 39.3202353.469353.428 0.018801418.8014 Vir-XX 327.606298.203298.201 -0.00356238 -3.56239 Mu-X -0.028926 0.3043560.30434 -1.08836e-05 -0.0108837 Lamb-System 1.2 0.000368363 0.000368248 -3.18082e-08 -3.18083e-05 Heat Capacity Cv: 12.4935 J/mol K (factor = 0.00115974) *** itle
Re: [gmx-users] NPT for compressing the system
Moeed wrote: Hello, Thanks for your reply. As for the simulation box, I did not change anything and I am still saying that I am having a cubic box of size 30nm. When I view the molecule in ngmx I see the cubic box.. no problem with that. What I was referring to was the option on menu bar where one can select type of box to view the trajecotry and using say triclinic box I see chain fits better (almost completely)in the box while in the case of cubic (which is my real box) I see molecules is not fitted completely inside the box.. I was just asking why is this happening. as you said none of that probably means anything . I think also it is unnecessary for now so please dont get confused. As I suspected. If you have a cubic box, you can certainly change a representation in any way you want, but it is meaningless. You've got a cube, plain and simple. As you requested I am including ALL the commands I used from the very beginning starting from replicating a 4C unit. editconf -f Eth4C.pdb -o Eth4C-d.gro -princ -d 0.058 -bt cubic editconf -f Eth4C-d.gro -o Eth4C-d-index.gro -n index.ndx -princ genconf -f Eth4C-d-index.gro -o Eth4C-d-index-rep30.gro -nbox 30 1 1 now I have PE chain of 60 units. using proper rtp and hdb files: pdb2gmx -f Eth4C-d-index-rep30-res.gro -o Eth4C-d-index-rep30-res-pdb2.gro -p Eth4C-d-index-rep30-res-pdb2.top -ff oplsaa output.pdb2gmx Then I EM this last gro file but since dimensions are 15 * 0.5 0.5 nm I am getting the error message : The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. then increased the size editconf -f Eth4C-d-index-rep30-res-pdb2.gro -o Eth4C-d-index-rep30-res-pdb2-boxsize30.gro -box 30 30 30 -angles 90 90 90 Then I EM the molecule with new box size 30nm and call this energy minimized structure PE60.gro. Now I want to replicate this chain. density demands 1 molecule in 5.76 nm3. As you said I forgot the density for a moment and took a large box. PE60 is already in a large enough box (30nm). this is all I did before doing any NPT. As for compressing the system to get more realistic structure and approaching the density I am after, I did several NPT runs. All show system is not equilbrated and they all crash and box does not become smaller than 2.2 nm. As you proposed I tried doing runs in stepwise manner. Below you see my trails: First trial :P 120 bar for 100 ps then P80 bar for 500 ps then P50 for 500 ps. this last run crashes at 2.2 nm size As Mark suggested I tried started with lower pressure: Second trail: P 50 for 500ps P40 bar for 500 ps P35 for 1000ps P30 for 1000 ps . Below is the results of this last run. before I had negative average Pressure but below the pressure is 30bar and real values fluctuate between -500 to 500 bar. T thermostat is working fine but LJ Columb terms not reaching equilibrium. Also box size is 2.7 nm which is larger than former trials.Molecule in not inside the box for almost the entire simulation.Only a small portion in inside and since it is long can not fit in. Understand that inside and outside are completely meaningless terms when using periodic boundary conditions. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions More problematic is if the molecule is so poorly oriented that it is interacting with itself through PBC, leading to spurious forces. The only way for anyone to help you better is probably through posting images. If you wish to do this, please follow the guidelines listed below (point number 3). http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette Do i need to start with lower pressures and go to higher values. Because the size is not changing that much with 30 bar? It seems to me that you may have found a stable state, but perhaps the configurations you're getting aren't appropriate (see above). Hard to say at this point. A different approach might be to simulate for a while first under NVT conditions, allowing your PE to collapse in on itself without the box quickly compressing around it. Then try your compression scheme on the structure that results from NVT. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] position restrain file
Hi all, Does anyone know how to mannually make a position restrain file? There is a protein and a dendrimer in my system. And I want the protein to be the reference group. Thank you in advance. Xiuping -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restrain file
Ping wrote: Hi all, Does anyone know how to mannually make a position restrain file? There is a protein and a dendrimer in my system. And I want the protein to be the reference group. http://www.gromacs.org/Documentation/Gromacs_Utilities/genrestr -Justin Thank you in advance. Xiuping -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hi How do I built the terminals of a peptide withe ACE and NHMe i.e.CH3CO and NHCH3 respectively. please suggest. My sequence is -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q- M. Baskar. -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
On 7/14/10 9:44 PM, munu...@yahoo.com wrote: Hi How do I built the terminals of a peptide withe ACE and NHMe i.e.CH3CO and NHCH3 respectively. please suggest. My sequence is -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q- M. Baskar. just add an extra residue (e.g. gly or ala) at eeither end using pymol or so, and then rename them in a text editor and throw away superfluous atoms. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
munu...@yahoo.com wrote: Hi How do I built the terminals of a peptide withe ACE and NHMe i.e.CH3CO and NHCH3 respectively. please suggest. My sequence is -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q- M. Baskar. http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources Note the last bullet point. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Phonon calculations in periodic crystals
I am trying to use GROMACS to calculate the phonons (normal modes) of a bulk crystal, CdSe. I have found a simple force field, Coulomb + Lennard-Jones, in the literature (Rabani, J. Chem. Phys. 116, 258, 2002) which the author showed reproduced the phonon dispersion curves and other mechanical properties of bulk wurtzite CdSe quite well. A number of other workers have used this force field in molecular dynamics simulations. But when I use Rabani's force field with GROMACS I get phonon frequencies that are much too high, up to about 2.2 times the experimental ones. I am doing all of my calculations with the double precision version of GROMACS. I have made a .top file for CdSe using Rabani's Lennard-Jones parameters and ionic charges, and a .gro file containing an integer number of unit cells with the known lattice constants. I first do an energy minimization until the maximum forces are around 1.e-4, and get the right crystal structure and lattice constants. I am using periodic boundary conditions with PME. I then use the nm integrator (with the -t option to read in the more precise .trr structure file) to calculate the Hessian, and then the g_nmeig_d program to diagonalize the Hessian and get the normal modes. This all seems to work fine, but I don't get the literature values for the frequencies (calculated maximum about 450 cm-1, literature and experimental about 215 cm-1). I have checked that when I enter the correct masses and known harmonic force constant for the H2 molecule, I get back the right vibrational frequency. I have tried changing the size of the system (5, 7, or 9 unit cells in each direction) and it has almost no effect on the frequencies. I have tried things like changing the Coulomb and Lennard-Jones cutoffs, and even tried regular Ewald rather than PME (which took a very long time), but these had no significant effect on my results. I also tried calculating the phonon spectrum for a different material, AgBr, using a Coulomb + Buckingham potential from the literature (J. Phys. Chem. 99, 14344, 1995). This gave me a better result, but still the distribution of frequencies is not correct and the maximum phonon frequency is about 15% higher than what the authors got with the same force field. Are you aware of any issues with GROMACS in doing normal mode calculations on periodic systems? Can you suggest any likely things I'm doing wrong? Anne Kelley Anne Myers Kelley Professor of Chemistry, School of Natural Sciences Secretary-Treasurer, APS Division of Laser Science University of California, Merced 5200 North Lake Road, Merced, CA 95343 Tel. 209-228-4345 amkel...@ucmerced.edu http://faculty.ucmerced.edu/amkelley/ -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: MD run for octanol system
Hi Esteban and Vitaly, Thanks for your respose, I tried trjconv with -pbc mol while generating movie and it worked this time. regards, vivek On 12 July 2010 16:01, Vitaly Chaban vvcha...@gmail.com wrote: Hmm... Straight lines... Is it VMD that your used to visualize the trajectory? I think this is just due to PBC. Compute some RDFs and they will give you an answer if your system is healthy. Dr. Vitaly Chaban I am trying to run MD simulation for octanol using GROMACS, I have downloaded the octanol.tar.gz from the user contributed section http://www.gromacs.org/@api/deki/files/18/=octanol.tar.gz. When I performed this MD run according to the run input file and molecule topology provided in this download, I observed straight lines in the system while visualizing the trajectory. Can anybody suggest if there is any problems in the run parameters provided or it is some mistake at my part ? As a first thought It seems like a boundary condition problem to me. Any insight into this will be really helpful for me. Is there any other source for getting required information for octanol. My final target is to run MD in water/octanol box. Please guide me with dos and donts, If anybody has attempted for the same. -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
