RE: [gmx-users] find the relevant structure out
I do not know how to extract some special frames out (professionally), so I just simply use vim to take the relevant models out and put into a new pdb file. Are there some good ways to extract one or two frames at the end of those whole frames? Base on your answering, now I start to suspect I might make something wrong cause I did it really clumsily. Thanks for your answering, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Wednesday, November 24, 2010 3:19 PM To: Discussion list for GROMACS users Subject: Re: RE: [gmx-users] find the relevant structure out - Original Message - From: #ZHAO LINA# zhao0...@e.ntu.edu.sg Date: Wednesday, November 24, 2010 17:52 Subject: RE: [gmx-users] find the relevant structure out To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, Thanks for your answering. Due to the difference in assignment, so I wonder which one I should build a bit much more faith on? I read (by eyes) the ss.xpm produced by do_dssp, and find the relevant resi out which showed as beta-sheet, but in pymol, it's really so standard alpha-helix, when I tried alter in pymol to show the beat-sheet as the way Justine mentioned in early email, it's really look weird. It's rather more likely that you're comparing two different (parts of) structures, than one secondary structure algorithm assigns sheet and one assigns helix to the same part of the same structure. Is the residue/atom numbering consistent. What does do_dssp say about the frame you cut out to give to pymol? Mark I noticed lots of paper they use DSSP to say something. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users- boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, November 24, 2010 1:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] find the relevant structure out Hi, Visualization software can sometimes assign the secondary structure incorrectly. There has been an interesting discussion on this on the Pymol user list years ago (http://www.mail-archive.com/pymol- us...@lists.sourceforge.net/msg01574.html).Secondary structure assignment is foremost human defined. You can use different metrics to obtain assignments, and should be careful to take any one of them as 'correct'. For instance, it makes a difference whether you assign three types (helical, sheet, loop), as Pymol does, or like seven types, as DSSP does. In pymol you can set the secondary structure type manually, but I find that the internal command 'dss' usually does a good job. Note that it only works on one frame and then uses the assignment for that frame on all of them, although there may be a workaround (I'll check; something with discrete_states). The frame to use for the assignment can be given to the 'dss' command through the argument state=N, where N is the frame number. If dss doesn't give the assignment you want, you can also try 'util.ss' that uses a different metric. Hope it helps, Tsjerk On 21/11/2010 11:43 PM, #ZHAO LINA# wrote: Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-) Mark 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A.
[gmx-users] perl script for g_hbond / summary_HBmap.dat
Dear Justin Thank you so much for help. I used # symbol in where you said and problem was solved. a output was obtained with name summary_HBmap.dat. this file is as follows: #DonorAcceptor% Exist. 5.478 NGL1 N NGL1H2 0.040 LYP2 HB2 LYP2 HG1 0.040 LYP2 O GLY3 H 6.158 GLN5 N GLN5CA 0.040 GLN5 C VAL6 N 0.040 VAL6 3HG2 VAL6 O 0.320 ARG7 HD2 ARG7HE 0.040 PHE8HA PHE8 HB1 8.517 PHE8 C SER9 N 1.439 ASN10CA ASN10CB 0.600 ASP11HA ASP11 HB1 0.040 GLN12 HB2 GLN12 HG1 0.440 THR13CB THR13 CG2 3.199 ILE14HB ILE14 1HG2 0.800 GLU15 H GLU15HA 3.798 LEU16 H LEU16HA 0.040 LEU16 3HD2 LEU16 O 0.040 GLU17 OE2 GLU17 O 2.279 LYP18 HD2 LYP18 HE130.508 LYP19 HB1 LYP19CG23.231 LYP19 C PHE20 N 0.840 PHE20HZ PHE20 HE2 0.040 GLU21 HG1 GLU21CD 0.480 THR22 2HG2 THR22 OG1 4.518 GLN23 HG2 GLN23 OE1 0.360 LYP24CG LYP24 HG2 0.120 TYR25 N TYR25CA 0.080 TYR25 CE2 TYR25 CD2 1.519 LEU26 CD1 LEU26 2HD110.716 SER27 HB1 SER27OG 3.958 PRO28 HB2 PRO28HA 0.120 PRO29CA PRO29 C 0.440 GLU30 OE1 GLU30 C11.955 17.193 NGL1 N 5.718 GLU30 N 7.837 SER27OG 1.279 SER27 N 6.078 LEU26 N 0.040 TYR25OH 0.080 TYR25 N49.100 LYP24NZ89.204 LYP24 N 7.917 GLN23 NE225.590 GLN23 N73.051 THR22 OG1 1.719 THR22 N93.882 GLU21 N 1.839 PHE20 N 0.200 LYP19NZ 0.040 I have some question: 1) when I used g_hbond for obtaining hbond.ndx and hbmap.xpm and hbond.log file, I selected two groups(1- protein nad 2- dna).In hbond.log and hbond.ndx file there are acceptors and donors belonging to both of protein and dna, while in my summary_HBmap.dat file both of donors and acceptors only belongs to protein. is there problem? 2) at the end of this file, there are only donors. what is means of %exist for these donors. This file should give me existence of each hbond during my trajectory and not donors. 3) I think that %exist should be determined for each of donor-hydrogen-acceptor being in hbond.ndx file.Isn't it? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?
Resolved: I have found the error. Apparently I was using -dt 20, and the condition that t mod dt = first time (ps) was not being met because the first time was a funny number. Have rectified it. Apologies for the inconvenience. -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU
Hi, On 11/24/10 2:59 AM, lin hen wrote: hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'Protein in water' 1 steps, 20.0 ps. Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.2# Post-simulation ~15s memtest in progress...done, no errors detected OpenMM run - timing based on wallclock. * NODE (s) Real (s) (%) Time: 90.796 90.796100.0 1:30 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.060 19.034 1.261* gcq#100: Jesus Can't Save You, Though It's Nice to Think He Tried (Black Crowes) The CPU version running results shows as following: ./mdrun Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.3# Average load imbalance: 4.7 % Part of the total run time spent waiting due to load imbalance: 2.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 % Parallel run - timing based on wallclock. * NODE (s) Real (s) (%) Time: 86.176 86.176100.0 1:26 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:741.634 35.849 20.054 1.197* gcq#0: Thanx for Using GROMACS - Have a Nice Day The gpu version looks *slower *than cpu version, does it make sense? Is there anyway I could optimize? In the default build, the CPU version will use all available cores on the machine and it's faster. 2. For the CPU benchmark dhfr-impl-1nm.bench, when I run : ./mdrun Back Off! I just backed up md.log to ./#md.log.9# Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) Starting 16 threads --- Program mdrun, VERSION 4.5.2 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.02425 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanx for Using GROMACS - Have a Nice Day Where could I modify this nodes#? Give the option -nt to mdrun to specify the number of threads you want to launch, e.g. $ mdrun -nt 8 3. for CPU benchmark dhfr-impl-inf.bench I modified cpu-imp-RF-inf.mdp: nsteps 1 grompp -f cpu-imp-RF-inf.mdp -o topol.tpr it will show: NOTE 1 [file cpu-imp-RF-inf.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... NOTE 2 [file topol.top, line 23568]: System has non-zero total charge: -1.10e+01 GB parameter(s) missing or negative for atom type 'H0' --- Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 870 Fatal error: Can't do GB electrostatics; the forcefield is missing 1 values for atomtype radii, or they might be negative . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Everybody's Good Enough For Some Change (LIVE) and when I run ./mdrun the steps still -1, infinite time How could I genete the right topol.tpr? Did you search the mailing lists? Copy and paste the error message in http://www.gromacs.org/Support/Mailing_Lists/Search and you will get a top hit http://lists.gromacs.org/pipermail/gmx-users/2010-September/053764.html You are using grompp 4.5.1 and mdrun 4.5.2 !? Remove all gromacs installs that you have, make a clean 4.5.3 install and try again. Rossen Thanks a lot. YY -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat
Quoting leila karami karami.lei...@gmail.com: Dear Justin Thank you so much for help. I used # symbol in where you said and problem was solved. a output was obtained with name summary_HBmap.dat. this file is as follows: #DonorAcceptor% Exist. 5.478 NGL1 N NGL1H2 0.040 LYP2 HB2 LYP2 HG1 0.040 LYP2 O GLY3 H 6.158 GLN5 N GLN5CA 0.040 GLN5 C VAL6 N 0.040 VAL6 3HG2 VAL6 O 0.320 ARG7 HD2 ARG7HE 0.040 PHE8HA PHE8 HB1 8.517 PHE8 C SER9 N 1.439 ASN10CA ASN10CB 0.600 ASP11HA ASP11 HB1 0.040 GLN12 HB2 GLN12 HG1 0.440 THR13CB THR13 CG2 3.199 ILE14HB ILE14 1HG2 0.800 GLU15 H GLU15HA 3.798 LEU16 H LEU16HA 0.040 LEU16 3HD2 LEU16 O 0.040 GLU17 OE2 GLU17 O 2.279 LYP18 HD2 LYP18 HE130.508 LYP19 HB1 LYP19CG23.231 LYP19 C PHE20 N 0.840 PHE20HZ PHE20 HE2 0.040 GLU21 HG1 GLU21CD 0.480 THR22 2HG2 THR22 OG1 4.518 GLN23 HG2 GLN23 OE1 0.360 LYP24CG LYP24 HG2 0.120 TYR25 N TYR25CA 0.080 TYR25 CE2 TYR25 CD2 1.519 LEU26 CD1 LEU26 2HD110.716 SER27 HB1 SER27OG 3.958 PRO28 HB2 PRO28HA 0.120 PRO29CA PRO29 C 0.440 GLU30 OE1 GLU30 C11.955 17.193 NGL1 N 5.718 GLU30 N 7.837 SER27OG 1.279 SER27 N 6.078 LEU26 N 0.040 TYR25OH 0.080 TYR25 N49.100 LYP24NZ89.204 LYP24 N 7.917 GLN23 NE225.590 GLN23 N73.051 THR22 OG1 1.719 THR22 N93.882 GLU21 N 1.839 PHE20 N 0.200 LYP19NZ 0.040 I have some question: 1) when I used g_hbond for obtaining hbond.ndx and hbmap.xpm and hbond.log file, I selected two groups(1- protein nad 2- dna).In hbond.log and hbond.ndx file there are acceptors and donors belonging to both of protein and dna, while in my summary_HBmap.dat file both of donors and acceptors only belongs to protein. is there problem? 2) at the end of this file, there are only donors. what is means of %exist for these donors. This file should give me existence of each hbond during my trajectory and not donors. Your output is total nonsense. Please refer to the header of the script for proper input. I suspect the problem is with the index file. You should NOT pass the entire hbond.ndx file to the script. 3) I think that %exist should be determined for each of donor-hydrogen-acceptor being in hbond.ndx file.Isn't it? It is, provided you pass proper input to the script. -Justin -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech
Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?
On 24/11/10 02:47, Mark Abraham wrote: On 24/11/2010 5:04 AM, ms wrote: On 23/11/10 17:00, Mark Abraham wrote: There is no general solution for bonds visualized on a single set of coordinates, however - over a trajectory, either molecules appear to diffuse out of the box, or appear to break. Yep, but if they appear broken because they are at the pbc boundaries is no big deal. The problem (and with this I answer also Florian Dommert) is that using -pbc tends to break stuff *inside* the box. That can't be true in general. Use of one of the five different -pbc options, possibly with -center and -ur, possibly over several invocations has always worked for anything I've wanted. However it's hard to answer an assertion that something is broken if you don't know what the person has tried :-) You are absolutely right, but well, it was not needed for the aestethic purposes so far required :) Of course if and when needed for analysis, I'll try harder with trjconv -pbc arcanes. thanks! m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] perl script for g_hbond / summary_HBmap.dat
Dear Justin thanks for your attention with chang of hbond.ndx file my problem was solved. I have another question about g_hbond: if I want to obtain same information (percentage of existence of each hbond during my trajectory) about water mediated hydrogen bonds between protein and dna, for obtaining of hbond.ndx and hbmap.xpm files from g_hbond tool, what groups should be select? in previous state (protein-dna direct hydrogen bond), I selected 1) protein and 2) dna. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Electric field: phosphate moves in the wrong direction
Dear users, I am applying an Electric Field along the z-axis to a system comprising a protein nanopore and a PO4- in order to see if gets into the pore. In some of the simulations the phosphate doesn't move on the opposite direction of the applied field but in the same direction! I wonder if anyone has experienced this behaviour and if you have any suggestions. What I can think of, is that the box might not be big enough, but I am not sure if that's the only reason. Thank you in advance, Susana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat
Hi, If you mean interactions bridged by a watermolecule, Protein-H2O-DNA, then I don't know of any gromacs related tools for this. You need to write your own tool for this. One way would be to multiply the existence functions for hbonds between protein and water and the hbonds between water and DNA, then use Justin's script to get the percentage. Erik leila karami skrev 2010-11-24 15.42: Dear Justin thanks for your attention with chang of hbond.ndx file my problem was solved. I have another question about g_hbond: if I want to obtain same information (percentage of existence of each hbond during my trajectory) about water mediated hydrogen bonds between protein and dna, for obtaining of hbond.ndx and hbmap.xpm files from g_hbond tool, what groups should be select? in previous state (protein-dna direct hydrogen bond), I selected 1) protein and 2) dna. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] installation
Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] installation
Quoting Rossella Noschese noschese.rosse...@gmail.com: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? You don't run GMXRC directly, you have to source GMXRC, but since you've already done that in your .bashrc, there's no need to do it again. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond -ac -life
Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB lifetime? any help will highly appreciated -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] installation
ok, but when I type luck it says command not found, where's my mistake? 2010/11/24 Justin A. Lemkul jalem...@vt.edu Quoting Rossella Noschese noschese.rosse...@gmail.com: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? You don't run GMXRC directly, you have to source GMXRC, but since you've already done that in your .bashrc, there's no need to do it again. -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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_hbond -ac -life
shahab shariati skrev 2010-11-24 16.24: Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB lifetime? any help will highly appreciated For hblife, I don't know. in hbac.xvg the first column is the autocorrelation function (acf) with a (somewhat dubious) correction to compensate for a finite system (the acf sohuld approac zero for large distances, but for a periodic finite system the tail is proprotional to 1/N, N being the number of particles). The second one is the 'raw' acf. Third column is the cross correlation between the hb-existence functions and corresponding contact-existence function (contacts fulfil the distace criterium but not the angular criterium). The fourth column is the derivative of the first column. The problem with -life, as far as I know, is that it models the hbond breaking/formation as a simple one step process, which may not be a good description. See the Luzar and Chandler papers for the theory behind the constants reported by g_hbond -ac. Therefore I'd use -ac to determine the rate for hb breaking. Cheers, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] installation
it was g_luck!!!it changed...ok, now it seems it wors! Thanks 2010/11/24 Rossella Noschese noschese.rosse...@gmail.com ok, but when I type luck it says command not found, where's my mistake? 2010/11/24 Justin A. Lemkul jalem...@vt.edu Quoting Rossella Noschese noschese.rosse...@gmail.com: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? You don't run GMXRC directly, you have to source GMXRC, but since you've already done that in your .bashrc, there's no need to do it again. -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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond -ac -life
Dear Erik thanks. thus -ac is only for determine the rate for hb breaking. is it true? or there is other usable case for -ac option? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] perl script for g_hbond / summary_HBmap.dat
Dear Erik I'm confused. is there h(t) in hbmap.xpm file? where is h(t)? which output file of g_hbond tool? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: perl script for g_hbond / summary_HBmap.dat
Hi, There is a bridging waters TCL script available for VMD which may be useful. It can be found at http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bridging_waters/ -- Tim Causgrove Associate Professor Texas AM University - Corpus Christi 6300 Ocean Drive, Unit 5802 Corpus Christi, TX 78412 361-825-2399 Date: Wed, 24 Nov 2010 18:37:45 +0330 From: leila karami karami.lei...@gmail.com Subject: [gmx-users] perl script for g_hbond / summary_HBmap.dat To: gmx-users gmx-users@gromacs.org Message-ID: aanlktikmoxojwnbffpcsbzywmbezjznjjwvsegjho...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear Erik and Justin Thank you so much for ypur help. yes I mean water mediated hydrogen bonds (protein-H2O-dna). since I'm beginner in perl script, please clarify your answer and explain more. what is your mean of existence functions exactly? do using of -ins option in g_hbond tool help me? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101124/42b2e41d/att achment-0001.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] installation
On Nov 24, 2010, at 4:04 PM, Rossella Noschese wrote: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: GMXRC is for setting the paths to your Gromacs executables. You can do that by typing source GMXRC, but this you have already done in your bashrc, so everything is already set up and fine! You will find all the Gromacs programs at your fingertips, e.g. mdrun -h prints out help for the main MD program. Carsten [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] (no subject)
Dear gromacs users, I want to heat system from 0K till 300K. Than do equilibration dynamics in water. I can not find any .mdp files where the system is gradually heated from initial temperature (0K) till needed temperature. I can only find NVP and NVT equilibration dynamics. Please can you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] (no subject)
Quoting Olga Ivchenko olga.ivche...@gmail.com: Dear gromacs users, I want to heat system from 0K till 300K. Than do equilibration dynamics in water. I can not find any .mdp files where the system is gradually heated from initial temperature (0K) till needed temperature. I can only find NVP and NVT equilibration dynamics. Please can you advice me on this? Please read in the manual about simulated annealing. There is even an example in the online manual (manual.gromacs.org). -Justin best, Olga 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] heme
Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_hbond -ac -life
shahab shariati skrev 2010-11-24 16.45: Dear Erik thanks. thus -ac is only for determine the rate for hb breaking. is it true? or there is other usable case for -ac option? And formation. And equillibrium constant. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat
Well, yes. The 'h' notation is never used in the xpm file. I just borrowed it from Luzar and chandler. Every line in the xpm data is the h(t) for a particular hydrogen bond. Erik leila karami skrev 2010-11-24 16.50: Dear Erik I'm confused. is there h(t) in hbmap.xpm file? where is h(t)? which output file of g_hbond tool? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] heme
shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Nose-Hoover Thermostat for Non Equilibrium Simulations
Hello GROMACS users, I have a questions regarding how a Nose-Hoover thermostat works in non equilibrium simulations in GROMACS . If I apply some constant acceleration in the x direction, is the thermostat applied to all degrees of freedom or is it applied only in the y and z direction. Thanks. Apoorv Graduate Student University of Illinois -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Martini parameters for formyl group
Dear users, I was wondering if there is Martini topology available for simple formyl (or aldehyde) group H - C = O. I would appreciate if somebody can direct me to the place where such force field parameters are discussed. Thanks, George -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA gek2...@med.cornell.edu Phone: 1-212-746-6539 Fax: 1-212-746-6226 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] heme
Erik Marklund wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? The same problem is frequently reported. The inter-residue bonds and angles are not assigned in pdb2gmx, nor are they present in the force field, IIRC. Hence the fatal errors. Perhaps something has changed since a long time ago, but I am sure problems exist in recent versions. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Reg: Interfacial tension
Hi all How to find the interfacial tension between two immiscible liquids in gromacs?. how one should start abou it. any help is highly is appreciated. Regards Vinoth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] heme
I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but Met SD and FE bond is not there. Shahid Nayeem On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul jalem...@vt.edu wrote: Erik Marklund wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? The same problem is frequently reported. The inter-residue bonds and angles are not assigned in pdb2gmx, nor are they present in the force field, IIRC. Hence the fatal errors. Perhaps something has changed since a long time ago, but I am sure problems exist in recent versions. -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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Reg: Interfacial tension
Hi all I want to calculate the interfacial tension of two immiscible liquids using the surface tension option in gromacs. when i do that i am getting the error message as One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off..I dont know what is it due to?. Below is my mdp file used for the mdrun. any help is highly appreciated. integrator = md nsteps= 50 dt = 0.002 nstxout= 1000 nstvout= 1000 nstenergy= 1000 nstlog= 1000 nstxtcout= 1000 xtc_precision= 1000 xtc_grps= system constraint_algorithm = shake constraints= none unconstrained_start= yes shake_tol= 0.0001 morse= no ns_type= grid nstlist= 5 rlist= 1.0 coulombtype= PME rcoulomb= 1.0 vdwtype= Cut-off rvdw= 1.0 pme_order= 4 fourierspacing= 0.16 pbc= xyz tcoupl= V-rescale tc-grps= system tau_t= 0.1 ref_t= 300 pcoupl= Berendsen pcoupltype= surface-tension tau_p= 1.0 1.0 ref_p= 5101.0 compressibility = 4.50e-50 DispCorr= EnerPres gen_vel= no Regards Vinoth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] RMSD and Resolution
Hi, Is there a relationship between RMSD value obtained from the calculation and Resolution value in PDB file? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
