Re: [gmx-users] g_h2order problem
Rongliang Wu wrote: Hello, gmx-users， my system has just 2827 water molecules, but the g_h2order command told me that there are more than 2807 waters in each slice. there are only one group in my index file and in O H H sequence. why? this is the sum over all frames. so this is normal. do it for a single frame to test it. the results are as follows: :-) G R O M A C S (-: Go Rough, Oppose Many Angry Chinese Serial killers :-) VERSION 3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_h2order (-: Option Filename Type Description -f 10ns.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb -n order_h2o.ndx InputIndex file -nm index.ndx Input, Opt. Index file -sbso20md.tpr InputGeneric run input: tpr tpb tpa xml -o order.xvg Output xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 2600 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -d string Z Take the normal on the membrane in direction X, Y or Z. -slint100 Calculate order parameter as function of boxlength, dividing the box in #nr slices. Reading file bso20md.tpr, VERSION 3.3 (single precision) Group 0 ( OW_HW1_HW2) has 8481 elements There is one group in the index Reading frame 0 time 2600.000 Box divided in 100 slices. Initial width o f slice: 0.103958 Reading frame1550 time 9980.000 Read trajectory. Printing parameters to file 91697 waters in slice 0 91534 waters in slice 1 91403 waters in slice 2 91630 waters in slice 3 90943 waters in slice 4 91577 waters in slice 5 91589 waters in slice 6 91367 waters in slice 7 91485 waters in slice 8 91641 waters in slice 9 91528 waters in slice 10 91599 waters in slice 11 91867 waters in slice 12 92253 waters in slice 13 92324 waters in slice 14 92318 waters in slice 15 91075 waters in slice 16 87944 waters in slice 17 82109 waters in slice 18 75151 waters in slice 19 67429 waters in slice 20 57285 waters in slice 21 42809 waters in slice 22 26212 waters in slice 23 12391 waters in slice 24 4453 waters in slice 25 1129 waters in slice 26 204 waters in slice 27 29 waters in slice 28 3 waters in slice 29 0 waters in slice 30 No water in slice 30 0 waters in slice 31 No water in slice 31 0 waters in slice 32 No water in slice 32 0 waters in slice 33 No water in slice 33 0 waters in slice 34 No water in slice 34 0 waters in slice 35 No water in slice 35 0 waters in slice 36 No water in slice 36 0 waters in slice 37 No water in slice 37 0 waters in slice 38 No water in slice 38 0 waters in slice 39 No water in slice 39 0 waters in slice 40 No water in slice 40 0 waters in slice 41 No water in slice 41 0 waters in slice 42 No water in slice 42 0 waters in slice 43 No water in slice 43 0 waters in slice 44 No water in slice 44 0 waters in slice 45 No water in slice 45 0 waters in slice 46 No water in slice 46 0 waters in slice 47 No water in slice 47 0 waters in slice 48 No water in slice 48 0 waters in slice 49 No water in slice 49 0 waters in slice 50 No water in slice 50 0 waters in slice 51 No water in slice 51 0 waters in slice 52 No water in slice 52 0 waters in slice 53 No water in slice 53 0 waters in slice 54 No water in slice 54 0 waters in slice 55 No water in slice 55 0 waters in slice 56 No water in slice 56 0 waters in slice 57 No water in slice 57 0 waters in slice 58 No water in slice 58 0 waters in slice 59 No water in slice 59 0 waters in slice 60 No water in slice 60 0 waters in slice 61 No water in slice 61 0 waters in slice 62 No water in slice 62 1 waters in slice 63 0 waters in slice 64 No water in
RE: [gmx-users] fep calculation of L-Asn - D-Asn transition
From: Alexandra Patriksson [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] fep calculation of L-Asn - D-Asn transition Date: Wed, 24 May 2006 11:11:38 +0200 Dear all, I'm trying to do a fep calculation of the L to D transition of a amino acid in a small peptide. We have done some changes to the dihedrals and the charges in the topology file (see below), but still we get dH/dlambda values that are far too large. Does anyone have an idea what could possibly be wrong? Have we forgotten something that should have been taken into account? Our changes in the toplogy file going from L - 0 : [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 7 opls_293B 1ASN CA 2 0.25 13.019 opls_293B 0 13.019 ; qtot 0.94 8 opls_140 1ASN HA 2 0.06 0 opls_1400 0 ; qtot 1 9 opls_136 1ASN CB 3 -0.12 14.027 opls_1360 14.027 ; qtot 0.88 10 opls_140 1ASNHB1 3 0.06 0 opls_1400 0 ; qtot 0.94 11 opls_140 1ASNHB2 3 0.06 0 opls_1400 0 ; qtot 1 [ dihedrals ] ; aiajakal functc0c1c2 c3 717 3 8 235 0 0 200 717 3 9 2-350 0 200 Our changes in the toplogy file going from 0 - D : [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 7 opls_293B 1ASN CA 2 0 13.019 opls_293B 0.25 13.019 ; qtot 0.94 8 opls_140 1ASN HA 2 0 0 opls_1400.06 0 ; qtot 1 9 opls_136 1ASN CB 3 0 14.027 opls_136 -0.12 14.027 ; qtot 0.88 10 opls_140 1ASNHB1 3 0 0 opls_1400.06 0 ; qtot 0.94 11 opls_140 1ASNHB2 3 0 0 opls_1400.06 0 ; qtot 1 [ dihedrals ] ; aiajakal functc0c1c2 c3 717 3 8 2 0 200 -35 0 717 3 9 2 0 200 35 0 I don't understand why you turned off the charges. Charge interactions are excluded anyhow for 1-3 interactions. The problem might be that just turning of the impropers does not have much effect, as the transition is blocked by the angle potentials. I would guess the D-L conversion would happen in one jump when the improper potential is high enough to overcome the barrier caused by the angle potentials. This would result in a large hysteresis. Turning of the angles (instead of the charges) might help. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CHARMM force field in GROMACS
Hi, I am making available under GPL two perl scripts, one of which converts a CHARMM27 .prm file into the necessary .itp files for pdb2gmx to use to produce .top files, and another that massages that .top file into something that will produce a .tpr file that will get CHARMM energy force evaluations. I have submitted it for inclusion on the GROMACS web page and hopefully it will appear there shortly. In the meantime, because I know there is interest in these scripts, if you want an email copy of the distribution that I hope will go up on the GROMACS web page, please email me off-list. Regards, Mark Abraham ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Simulating crystalls
I am trying to simulate a crystal too. I have a box size of .65 nm and there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm. I get a segmentation fault after mdrun -v. Is an atom with co-ordinates 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system? What I am trying to ask is, does GROMACS consider these as 2 different atoms placed at the respective positions or do the 2 atoms overlap? What could be the reason for the segmentation fault? Is it because the atoms are too close to each other? - Karamyog.On 5/23/06, Mark Abraham [EMAIL PROTECTED] wrote: David van der Spoel wrote: Gale, Ella wrote: Thanks for the advice, but my force-field has no charges and hence no coulomb potential, so I want the atoms to interact with itself via the Van der Waals functions. I'm using 3.2.1 at the moment and there is no option to use any of the Ewald summation techniques. Is this something that has been added in the most recent version? Ewald variant are only for Coulomb so far. You can use a normal cutoff or a shifted cutoff.One or two of the early PME papers describe implementation details forLJ PME, but I am not immediately aware of a modern MD code that implements it. If you want it, shop around.Mark___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Position restrain
Alessandro Mattozzi wrote: Hi How should my posres.itp look like? Is there any template available? Thank Regards genpr does generate position rstrains ... -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-page: http://md.chem.rug.nl/~periole -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Stange results of bonds fep
Dear all, I'm trying to calculate dG of transition between alpha and pi conformation in some part of my protein. I indended to use fep and perform this conversion in three steps: first, I want to fix alpha conformation gradually by indroducing bonded interactions between i'th H, i+4 and i+5'th O, then change equlibrium distances of these bonds from alpha- to pi- state and finally remove bonds. Surpringly, my system behaved in quite unusual way : at the first steps of simulation (I used slow growth fep) distances between perturbed atoms increased dramatically from 0.2nm and 0.45nm (which are equlibrium distances for alpha-state) to 0.7 nm and even further. No increase, however, was mentioned when fep was turned off. I succeeded to reproduce this strange behaviour on smaller systems by cutting the piece of the protein, converting it into poly-cly chain and performing the same simulation with following parameters f A and B state: [ atoms ] ... 16 opls_236 2GLY O 4 -0.515.9994 ; qtot 1 ... 23 opls_236 3GLY O 6 -0.515.9994 ; qtot 1 ... 46 opls_241 7GLY H 130.3 1.008 ; qtot 0.8 ... [ bonds ] ... 2346 1 0.200 0.201000 1646 1 0.450 0.451000 At the and of 50 ps bd simulation from lambda=0 to lambda=1 distance between 23 and 46 atoms increased from 0.196 to 0.448 nm, and distance between 16 and 46 atoms increased form 0.496 to 0.73 nm. Can anyone suggest, why results of fep are so strange? Is this a bug or I'm missing something? P.S. I run all these tests with gromacs 3.3.1 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] POPC simulation
Hi Steffen, thanks for the reply. this is what i have done. my topol.top looks like this now #inlcude ffgmx.itp inlcude popc.itp. as per your last reply i have copied the contents of lipid.itp to ffgmxbon.itp and ffgmxnb.itp without removing the contents of the respective file. basically just appended the files with the contents of the lipid.itp . now when i run grommp -v - -f em.mdp , it still says atom type LC3 not found,. i can't understand why this mistake in fact taking place. popc.itp file the first 3 lines after [atom] in fact mentions LC3. so where is the mistake. plx help. thanks. arindam ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Simulating crystalls
Mark Abraham [EMAIL PROTECTED] writes: David van der Spoel wrote: Gale, Ella wrote: Thanks for the advice, but my force-field has no charges and hence no coulomb potential, so I want the atoms to interact with itself via the Van der Waals functions. I'm using 3.2.1 at the moment and there is no option to use any of the Ewald summation techniques. Is this something that has been added in the most recent version? Ewald variant are only for Coulomb so far. You can use a normal cutoff or a shifted cutoff. One or two of the early PME papers describe implementation details for LJ PME, but I am not immediately aware of a modern MD code that implements it. If you want it, shop around. Mark I got to read a note by Cheatham on PME for LJ VDW. Look for question Is there a PME algorithm also for the VDW interactions? in http://amber.scripps.edu/Questions/ewald.html Yang Ye ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC simulation
Arindam, I fixed this problem a while ago and it was pretty difficult to figure out. I tinkered with so many things, once I got it to work I didn't even know what steps I took to fix it! Here's something to try: GROMACS doesn't like the fact popc.itp has a four-character residue name (since protein residues are just three characters). If you look at your .gro file, you'll probably see that somewhere along the line, the POPC got truncated to POP. Try changing all instances of 'POPC' to 'POP' in your setup--this should probably just be in popc.itp (lots of occurrences) and topol.top(one occurrence where you list the number of POP molecules. Please let me know if that works. Jim On May 24, 2006, at 1:02 PM, Arindam Ganguly wrote: Hi Steffen, thanks for the reply. this is what i have done. my topol.top looks like this now #inlcude ffgmx.itp inlcude popc.itp. as per your last reply i have copied the contents of lipid.itp to ffgmxbon.itp and ffgmxnb.itp without removing the contents of the respective file. basically just appended the files with the contents of the lipid.itp . now when i run grommp -v - -f em.mdp , it still says atom type LC3 not found,. i can't understand why this mistake in fact taking place. popc.itp file the first 3 lines after [atom] in fact mentions LC3. so where is the mistake. plx help. thanks. arindam ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC simulation
/pipermail/gmx-users/attachments/ 20060524/362cca6e/attachment-0001.html -- Message: 3 Date: Wed, 24 May 2006 17:13:09 +0200 From: Alessandro Mattozzi [EMAIL PROTECTED] Subject: [gmx-users] Position restrain To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi How should my posres.itp look like? Is there any template available? Thank Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060524/ b7718570/attachment-0001.html -- Message: 4 Date: Wed, 24 May 2006 17:21:11 +0200 From: Xavier Periole [EMAIL PROTECTED] Subject: Re: [gmx-users] Position restrain To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii; format=flowed Alessandro Mattozzi wrote: Hi How should my posres.itp look like? Is there any template available? Thank Regards genpr does generate position rstrains ... -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-page: http://md.chem.rug.nl/~periole -- -- Message: 5 Date: Wed, 24 May 2006 19:55:20 +0400 From: Oleg Stroganov [EMAIL PROTECTED] Subject: [gmx-users] Stange results of bonds fep To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii Dear all, I'm trying to calculate dG of transition between alpha and pi conformation in some part of my protein. I indended to use fep and perform this conversion in three steps: first, I want to fix alpha conformation gradually by indroducing bonded interactions between i'th H, i+4 and i+5'th O, then change equlibrium distances of these bonds from alpha- to pi- state and finally remove bonds. Surpringly, my system behaved in quite unusual way : at the first steps of simulation (I used slow growth fep) distances between perturbed atoms increased dramatically from 0.2nm and 0.45nm (which are equlibrium distances for alpha-state) to 0.7 nm and even further. No increase, however, was mentioned when fep was turned off. I succeeded to reproduce this strange behaviour on smaller systems by cutting the piece of the protein, converting it into poly-cly chain and performing the same simulation with following parameters f A and B state: [ atoms ] ... 16 opls_236 2GLY O 4 -0.5 15.9994 ; qtot 1 ... 23 opls_236 3GLY O 6 -0.5 15.9994 ; qtot 1 ... 46 opls_241 7GLY H 130.3 1.008 ; qtot 0.8 ... [ bonds ] ... 2346 1 0.200 0.201000 1646 1 0.450 0.451000 At the and of 50 ps bd simulation from lambda=0 to lambda=1 distance between 23 and 46 atoms increased from 0.196 to 0.448 nm, and distance between 16 and 46 atoms increased form 0.496 to 0.73 nm. Can anyone suggest, why results of fep are so strange? Is this a bug or I'm missing something? P.S. I run all these tests with gromacs 3.3.1 -- Message: 6 Date: Wed, 24 May 2006 12:02:43 -0500 From: Arindam Ganguly [EMAIL PROTECTED] Subject: [gmx-users] POPC simulation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Steffen, thanks for the reply. this is what i have done. my topol.top looks like this now #inlcude ffgmx.itp inlcude popc.itp. as per your last reply i have copied the contents of lipid.itp to ffgmxbon.itp and ffgmxnb.itp without removing the contents of the respective file. basically just appended the files with the contents of the lipid.itp . now when i run grommp -v - -f em.mdp , it still says atom type LC3 not found,. i can't understand why this mistake in fact taking place. popc.itp file the first 3 lines after [atom] in fact mentions LC3. so where is the mistake. plx help. thanks. arindam -- Message: 7 Date: Wed, 24 May 2006 15:53:07 + (UTC) From: Yang Ye [EMAIL PROTECTED] Subject: [gmx-users] Re: Simulating crystalls To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii Mark Abraham [EMAIL PROTECTED] writes: David van der Spoel wrote: Gale, Ella wrote: Thanks for the advice, but my force-field has no charges and hence no coulomb potential, so I want the atoms to interact with itself via the Van der Waals functions. I'm using 3.2.1 at the moment and there is no option to use any of the Ewald
RE: [gmx-users] g_h2order still makes problem
the g_h2order still makes problem, i divided the box into 1 slice but it told me there are 2405777 water in the slice while the system has only 2827 tip4p water molecules. and the mu and cos generated is tortured! can it be any mistakes from the index? my index file has only one group of the sequence OW HW1 HW2, the shell is not included. Didn't David just reply yesterday and say that that number is a sum of all terms over the entire trajectory being analysed? i.e. if you analysis a single FRAME (not slice), then the number should correspond to the number of waters in there. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dipoles -slab option
Hello everyone,
Water tends to align at a hydrophobic surface in a way to maximize H-bonds.
Doing this leads to a dipole moment that is perpendicular to the surface
(pointing away from the surface). Is this correct?
I'm trying to verify this with a simulation. I have an uncharged surface in the
xz-plane. I'm using g_dipoles with the -slab option to get the dipole moment of
water slabs in the y direction. Below is the output. There are 5 columns of data
for some reason and I can't interepret it. The first column is the position of
the water slab. I can only assume that column 2 is the dipole in the x
direction and column 3 is the dipole in the y direction and so on. Is that
correct? What is the last column for?
@title Average dipole moment per slab
@xaxis label Box-Y (nm)
@yaxis label \f{12}m\f{4} (D)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend \f{12}m\f{4}\sX\N
@ s1 legend \f{12}m\f{4}\sY\N
@ s2 legend \f{12}m\f{4}\sZ\N
0.500 0.000 0.000 0.000 0.000
1.500 -46.367 3.869 41.074 62.064
2.500 36.106 0.765 3.870 36.321
3.500 7.638 0.371 1.223 7.744
4.500 -18.688 1.380 -20.000 27.406
5.500 8.237 4.201 -9.015 12.914
6.500 -0.103 0.057 -0.023 0.119
7.500 0.000 0.000 0.000 0.000
8.500 0.000 0.000 0.000 0.000
9.500 0.000 0.000 0.000 0.000
Thanks,
Bob Johnson
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Re: [gmx-users] Simulating crystalls
karamyog singh wrote: I am trying to simulate a crystal too. I have a box size of .65 nm and there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm. I get a segmentation fault after mdrun -v. Is an atom with co-ordinates 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system? Cubic PBC with side length l means that (x,y,z) is equivalent to (x+al,y+bl,z+cl) for any integers a,b and c. What I am trying to ask is, does GROMACS consider these as 2 different atoms placed at the respective positions or do the 2 atoms overlap? No. GROMACS takes every atom you give in the .top file and uses it - there is no attempt to check for symmetry simplifications such as quantum chemistry codes do. What could be the reason for the segmentation fault? Is it because the atoms are too close to each other? You're on your own here unless you can provide more information. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dipoles -slab option
+++ Bob Johnson [Wed, May 24, 2006 at 08:37:01PM -0400]: for some reason and I can't interepret it. The first column is the position of the water slab. I can only assume that column 2 is the dipole in the x direction and column 3 is the dipole in the y direction and so on. Is that correct? What is the last column for? The last column is the vector norm. 1.500 -46.367 3.869 41.074 62.064 $ perl -e 'print sqrt((-46.367)**2 + 3.869**2 + 41.074**2)' 62.0640099091253 -- Groeten, Paul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
