[gmx-users] Order parameter for unsaturated lipid chain in UA model
Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two recently emails: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html , but I am still in doubt. So my question is regarding the unsaturated lipid chain of POPC. I would like to calculate the order parameters for my united atoms so I make first an index file with the tail atoms from the carbonyl-C to the methyl-C and then I run g_order -od. Then I make a new index file with the two atoms of the double bond and the atom before and after the double bond (four atoms in total) running g_order -unsat -od I then take the two values from the last g_order run and replace them with the order parameters for the double bond calculated without -unsat. When looking at the graph and comparing to the literature this graph it looks wrong: First there is a small dip in the order for the atom before the double bond, then it goes a bit up for the first double bonded C, and then for the next double bonded C and the atom after that the order is quite low. I know this description is not good, but it was just to explain, that the graph is not as expected. I would very much appreciated if anyone could tell me, where I go wrong. Thank you, Sarah -- 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
SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Thank you for your quick respons! It is not so much the drop, but more the position and the prescens of a small drop, then a little rise and then the big drop. I have pasted the file in below. Do you think my method of replacing the order parameters for the double bonded atoms is ok? Order parameters sn-2 chain POPC* 1 0.176177 20.18184 3 0.182874 4 0.180724 5 0.167932 6 0.162731 7 0.107512 8 0.139351 9 0.0311607 10 0.0519802 11 0.095191 12 0.0884555 13 0.0930531 14 0.0787042 15 0.0732823 16 0.0541174 ** Thank you, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: to 25-02-2010 14:42 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel Sarah Witzke wrote: Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two recently emails: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html , but I am still in doubt. So my question is regarding the unsaturated lipid chain of POPC. I would like to calculate the order parameters for my united atoms so I make first an index file with the tail atoms from the carbonyl-C to the methyl-C and then I run g_order -od. Then I make a new index file with the two atoms of the double bond and the atom before and after the double bond (four atoms in total) running g_order -unsat -od I then take the two values from the last g_order run and replace them with the order parameters for the double bond calculated without -unsat. When looking at the graph and comparing to the literature this graph it looks wrong: First there is a small dip in the order for the atom before the double bond, then it goes a bit up for the first double bonded C, and then for the next double bonded C and the atom after that the order is quite low. I know this description is not good, but it was just to explain, that the graph is not as expected. I would very much appreciated if anyone could tell me, where I go wrong. I don't see why a drop in the order parameter is unexpected. I see it all the time in published papers of unsaturated lipids, for example: http://pubs.acs.org/doi/abs/10.1021/jp902131b http://www3.interscience.wiley.com/journal/114209721/abstract -Justin Thank you, Sarah -- 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 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] spc vs. flex_spc
Dear gmx-users, I am wondering whether or not there is a good reason to use flex_spc during energy minimisation and spc during production run? I guess one would not use flex_spc during a production run as this would decrease the time step needed quite a lot - but is it a good idea to use during EM as the system easier relaxes? I know that strictly this is not a gromacs related issue, but if you could say just 'yes' or 'no', I would very much appreciate it. Thank you for all your help and quick answers, Sarah -- 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
SV: [gmx-users] spc vs. flex_spc
Thank you very much for your quick answer Berk! Fra: gmx-users-boun...@gromacs.org på vegne af Berk Hess Sendt: ma 15-02-2010 10:56 Til: Discussion list for GROMACS users Emne: RE: [gmx-users] spc vs. flex_spc Hi, flex_spc is not a reliable water model, never use it for MD. You should only use it when your initial configuration is so bad that energy minimization with normal, rigid water molecules crashes. However, the deviations are so small that after a few picoseconds of MD with normal spc there will be no memory of the flex_spc initial structure. Berk Date: Mon, 15 Feb 2010 10:38:40 +0100 From: sawi...@student.sdu.dk To: gmx-users@gromacs.org Subject: [gmx-users] spc vs. flex_spc Dear gmx-users, I am wondering whether or not there is a good reason to use flex_spc during energy minimisation and spc during production run? I guess one would not use flex_spc during a production run as this would decrease the time step needed quite a lot - but is it a good idea to use during EM as the system easier relaxes? I know that strictly this is not a gromacs related issue, but if you could say just 'yes' or 'no', I would very much appreciate it. Thank you for all your help and quick answers, Sarah -- gmx-users mailing list gmx-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 New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop -- 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] Closing of .trr and .edr files after running out of space
Dear gmx-users, I have been very unfortunate (and stupid): I was running a simulation of 220 ns and due to limited space at our cluster-computer I was writing the .trr file and .edr file directly to another disc. That was un-clever since I did not write the .cpt file to that disc as well. As I am not the only one using the storage disc it ran out of space very shortly before the end of my simulation and I got this error message in the .log file: Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 DMPC-DMPC2.60809e+022.19979e+023.95442e+027.50289e+01 DMPC-SOL6.74362e+022.11485e+020.0e+000.0e+00 SOL-SOL9.65717e+026.15314e+020.0e+000.0e+00 T-DMPC T-SOL 2.81532e+001.30102e+00 --- Program mdrun_mpi, VERSION 4.0.4 Source code file: enxio.c, line: 212 File input/output error: Cannot close energy file; it might be corrupt, or maybe you are out of quota? --- I guess it is unable to close due to a lack of space? When running gmxcheck on the generated .trr file this message was printed: Checking file dmpc.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 10.000 # Atoms 35513 Reading frame4000 time 40010.000 --- Program gmxcheck, VERSION 4.0.4 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- This .trr file should be 220 ns and 18 G big, it is now 15 G. Even though the .cpt file is only set to update every 15 min (default) there is only 3 min between state_previous.cpt and state.cpt. I think it is because it wrote a new .cpt just when finishing the run? But then non of the .cpt files are old enough to allow rerun from the point of the problem. Stupid of me. Now, the simulations was supposed to be of 220 ns, but actually I only need around 150 ns for my purpose. So my question is whether there is anyy way to close the .trr file at the point it is at and then have a functional .trr file? Best regards, Sarah -- 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] Closing of .trr and .edr files after running out ofspace
Thank you very much, that was a good idea! I tried ~/gromacs-4.0.4/bin/trjconv -f dmpc.trr -e 15 -o dmpc-150ns.trr to get the first 150 ns out of the simulation. Trjconv writes this to me: Will write trr: Trajectory in portable xdr format trn version: GMX_trn_file (single precision) - frame 4210 time 42110.004- frame 4000 time 40010.000 --- Program trjconv, VERSION 4.0.4 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- When checking the new .trr file by ~/gromacs-4.0.4/bin/gmxcheck -f dmpc-150ns.trr the output is: Checking file dmpc-150ns.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 10.000 # Atoms 35513 Reading frame4000 time 40010.000 Item#frames Timestep (ps) Step 422010 Time 422010 Lambda422010 Coords422010 Velocities422010 Forces 0 Box 422010 So this means that the .trr only conatins 42.2 ns, right? Best, Sarah -Original Message- From: gmx-users-boun...@gromacs.org on behalf of chris.ne...@utoronto.ca Sent: Tue 09-02-2010 16:38 To: gmx-users@gromacs.org Subject: [gmx-users] Closing of .trr and .edr files after running out ofspace trjconv -e for the .trr eneconv -e for the .edr --original message -- Dear gmx-users, I have been very unfortunate (and stupid): I was running a simulation of 220 ns and due to limited space at our cluster-computer I was writing the .trr file and .edr file directly to another disc. That was un-clever since I did not write the .cpt file to that disc as well. As I am not the only one using the storage disc it ran out of space very shortly before the end of my simulation and I got this error message in the .log file: Epot (kJ/mol)Coul-SR LJ-SRCoul-14 LJ-14 DMPC-DMPC2.60809e+022.19979e+023.95442e+027.50289e+01 DMPC-SOL6.74362e+022.11485e+020.0e+000.0e+00 SOL-SOL9.65717e+026.15314e+020.0e+000.0e+00 T-DMPC T-SOL 2.81532e+001.30102e+00 --- Program mdrun_mpi, VERSION 4.0.4 Source code file: enxio.c, line: 212 File input/output error: Cannot close energy file; it might be corrupt, or maybe you are out of quota? --- I guess it is unable to close due to a lack of space? When running gmxcheck on the generated .trr file this message was printed: Checking file dmpc.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 10.000 # Atoms 35513 Reading frame4000 time 40010.000 --- Program gmxcheck, VERSION 4.0.4 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- This .trr file should be 220 ns and 18 G big, it is now 15 G. Even though the .cpt file is only set to update every 15 min (default) there is only 3 min between state_previous.cpt and state.cpt. I think it is because it wrote a new .cpt just when finishing the run? But then non of the .cpt files are old enough to allow rerun from the point of the problem. Stupid of me. Now, the simulations was supposed to be of 220 ns, but actually I only need around 150 ns for my purpose. So my question is whether there is anyy way to close the .trr file at the point it is at and then have a functional .trr file? Best regards, Sarah -- 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
[gmx-users] Principal axis (g_principal)
Dear gmx users, I am doing several analyses (version 4.0.4) on my simulations with small organic molecules inserting into a DMPC bilayer. Now I would like to calculate whether the small molecule inserts into the membrane with a specific angle to the membrane normal (or z-axis). I have used two approaches: 1) My molecule is a cyclohexene ring with two para substituents. I made an index group with carbon number 3 and number 10 (in different groups) which corresponds to the first substituent-atoms on each side of the ring. This vector describes the shape of the molecule quite well. I then used g_bundle to calculate the angle between this vector and the z-axis by echoing first the C3-group and then the C10-group: echo 0 1 | g_bundle -f xxx.xtc -s xxx.tpr -n xxx-vector.ndx -na 1 -z -ot xxx-vector.xvg This gives fairly reasonable results and angle distribution. 2) I also calculated the principal axis by g_principal where I echoed each small molecule as a whole: echo 0 | g_principal -f xxx.xtc -s xxx-1.tpr -n xxx-lim.ndx -a1 xxx-principal.dat -a2 xxx-axis2.dat -a3 xxx-axis3.dat To get the angle between the principal axis and the z-axis one takes the arcos the the z-component. This created quite a different and very broad angle distribution. This puzzled me very much since the difference between the C3-C10 vector and the principal axis should not be that great. I then used a small python program to calculate the principal axis of my molecule and the result was again quite different than from g_principal. I have tried to rotate each of my substituent groups by 120 degrees (creating 9 different conformations) and then calculate the difference in the principal axis but this creates only a deviation of max. 16-17 degrees not at all accounting for the very different angle distributions seen. I have not included numbers but I can do so along with the python code. I would like to ask if anyone can see any obvious mistakes or know of something special to be aware of when using g_principal? Thank you, Sarah -- 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
SV: SV: SV: SV: [gmx-users] g_saltbr
Sarah Witzke wrote: snip In each of the files are a set of distances as a function of time - it does not seem that strange, that the size is equal then. When I plot for instance the four .xvg files mentioned above I get four different curves. Also diff lists that every line is different. I really don't understand what I'am doing wrong. I don't know that you are necessarily doing anything wrong, but it's hard to diagnose the potential problems without actually seeing what might be in those .xvg files. Can you post short snippets of a few of them, just to demonstrate what the difference is? I am wondering if there is so much memory required, that the calculation is dumping out the resulting data prematurely and therefore over-writing incomplete output files. Just a guess, but worth considering. Before I got to answer this email, Tsjerk posted what I think is the answer. Here is though four files with the same name except the #s. They are only for the last 10 ns with -dt 1000 to shorten them: :: sb-DMPC191:DMPC192.xvg :: # This file was created Wed Dec 2 00:56:33 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr -f dmpcdpac32na32-all.xtc -s dmpcdpac32na32-1.tpr -b 21 -dt 1000 -sep # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr is part of G R O M A C S: # # Good gRace! Old Maple Actually Chews Slate # @title sb-DMPC191:DMPC192.xvg @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy 21 3.54172 211000 3.63549 212000 3.82094 213000 3.87692 214000 3.72715 215000 3.69254 216000 3.76674 217000 3.5567 218000 3.4372 219000 3.49882 22 3.35077 :: #sb-DMPC191:DMPC192.xvg.1# :: # This file was created Wed Dec 2 00:56:33 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr -f dmpcdpac32na32-all.xtc -s dmpcdpac32na32-1.tpr -b 21 -dt 1000 -sep # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr is part of G R O M A C S: # # Good gRace! Old Maple Actually Chews Slate # @title sb-DMPC191:DMPC192.xvg @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy 21 2.96721 211000 3.69049 212000 3.77841 213000 3.28861 214000 3.10005 215000 2.96617 216000 3.12796 217000 3.48478 218000 3.62286 219000 3.64729 22 3.42346 :: #sb-DMPC191:DMPC192.xvg.2# :: # This file was created Wed Dec 2 00:56:33 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr -f dmpcdpac32na32-all.xtc -s dmpcdpac32na32-1.tpr -b 21 -dt 1000 -sep # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr is part of G R O M A C S: # # Good gRace! Old Maple Actually Chews Slate # @title sb-DMPC191:DMPC192.xvg @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy 21 3.34607 211000 3.72107 212000 3.73002 213000 3.57064 214000 3.42572 215000 3.34358 216000 3.45839 217000 3.41128 218000 3.91261 219000 3.99654 22 3.77672 :: #sb-DMPC191:DMPC192.xvg.3# :: # This file was created Wed Dec 2 00:56:33 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr -f dmpcdpac32na32-all.xtc -s dmpcdpac32na32-1.tpr -b 21 -dt 1000 -sep # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr is part of G R O M A C S: # # Good gRace! Old Maple Actually Chews Slate # @title sb-DMPC191:DMPC192.xvg @xaxis label Time (ps) @yaxis label Distance (nm) @TYPE xy 21 3.1681 211000 3.62663 212000 3.85572 213000 3.58639 214000 3.38853 215000 3.31324 216000 3.43343 217000 3.27437 218000 3.14695 219000 3.15015 22 3.00437 Thank you again for all your help! Sarah -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 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
SV: SV: SV: SV: [gmx-users] g_saltbr
Hi Tsjerk and others,
This is a very good explanation! Thank you. Did you mean I should file a bug
report or are you doing it since you understand the code?
Thank you all!
Sarah
Fra: gmx-users-boun...@gromacs.org på vegne af Tsjerk Wassenaar
Sendt: on 02-12-2009 19:29
Til: jalem...@vt.edu; Discussion list for GROMACS users
Emne: Re: SV: SV: SV: [gmx-users] g_saltbr
Hi,
Of course the real answer is in the code...
if (bSep) {
snew(buf,256);
for(i=0; (incg); i++)
for(j=i+1; (jncg); j++) {
if (nWithin[i][j]) {
sprintf(buf,sb-%s:%s.xvg,cg[i].label,cg[j].label);
fp=xvgropen(buf,buf,Time (ps),Distance (nm));
...
So, a file is opened for each combination of charge(d) groups for
which the distance is lower than the cut-off, at least once in the
trajectory. The label is a property of the charge group, and is set
somewhere before:
sprintf(buf,%s%d,*(atoms-resname[resnr]),resnr+1);
cg[ncg].label=strdup(buf);
Althogether, this just means that you have multiple charge(d) groups
per residue, which are assigned the same label. Let's see, a phosphate
and a choline, two residues, 2*2=4 possible salt bridges between them.
Seems to add up, doesn't it? Probably should be considered a bug
though. Better file it...
Cheers,
Tsjerk
On Wed, Dec 2, 2009 at 7:10 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Sarah Witzke wrote:
snip
In each of the files are a set of distances as a function of time - it
does not seem that strange, that the size is equal then.
When I plot for instance the four .xvg files mentioned above I get four
different curves. Also diff lists that every line is different.
I really don't understand what I'am doing wrong.
I don't know that you are necessarily doing anything wrong, but it's hard to
diagnose the potential problems without actually seeing what might be in
those .xvg files. Can you post short snippets of a few of them, just to
demonstrate what the difference is? I am wondering if there is so much
memory required, that the calculation is dumping out the resulting data
prematurely and therefore over-writing incomplete output files. Just a
guess, but worth considering.
-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
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--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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SV: [gmx-users] g_saltbr
Dear gmx users, I'm sorry to continue an old thread - here's a summary: I have a DMPC bilayer surrounded by water and a small organic molecule with a deprotonated carboxylic acid. The small molecule diffuses near the membrane interface/into the membrane. I would like to calculate any formed salt bridge between the negative carboxylic acid of the small molecule and the positive charge of the DMPC choline nitrogen. To do this I use these two commands: g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 10 g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 10 -sep The first command I use to get the files min-min.xvg, plus-plus.xvg and plus-min.xvg. Here I am interested in plus-min.xvg to tell me which of the salt bridges between the small molecule and DMPC is between the negative acid and the positive choline (as opposed to between the negative acid and the negative phosphate of DMPC). Then I run the command again with -sep to get the individual graphs of each interaction. This is unfortunately a rather tedious exercise since very many files are generated for all sort of charged interactions (DMPC-DMPC, smallmolecule-smallmolecule, counterion-counterion, and pairs thereof), and then I have to select the wanted ones by looking through plus-min.xvg. I guess I could make some sort of script to make it easier, but I just want to check if there is absolutely no way to include an .ndx file or only choose plus-min interactions? Another thing, when running the second command several of each files are generated, for instance: sb-DMPC144:DMPC154.xvg #sb-DMPC144:DMPC154.xvg.3# Etc The files are not identical when checked with diff or looked at in xmgrace. I suppose the last generated files are the correct one, but what are all the other files? Thank you in advance, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Sarah Witzke Sendt: fr 20-11-2009 14:55 Til: jalem...@vt.edu; Discussion list for GROMACS users Emne: RE: [gmx-users] g_saltbr -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Fri 20-11-2009 14:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_saltbr Sarah Witzke wrote: Dear gromacs users, First of all thank you for all your previous help! I have a new question regarding an analysis of ionic interactions between DMPC lipids and a small molecule with a deprotonated carboxylic acid. g_saltbr takes as input an .xtc file and a .tpr file and from these files it measures the distance between all charged groups and create the three files min-min.xgv, plus-plus.xvg and min-plus.xvg. My bilayer contains 128 DMPC molecules each having a positively charge and a negative charge. The small molecule has one negative charge. Running g_saltbr -f xxx.xtc -s xxx.tpr -sep -b 10 -t 0.5 puts the distances between charged atoms in separate files, which is what I would like. But now the files are named like this: sb-small molecule'number':DMPC'number'.xvg How can I then know whether the small molecule is interacting with a positive atom in DMPC (like plus-min) or a negative atom in DMPC (like min-min)? If you omit the -sep option, you'll get plus-min.xvg, min-min.xvg, and plus-plus.xvg. In these, you will find the different groups that interact through these different charge interactions. OK. One more question is on the distance: From this mail I read that the distance calculated is between the charged atoms, not the COM of the charge group: http://lists.gromacs.org/pipermail/gmx-users/2005-June/015811.html Then what about my small molecule with the deprotonated acid? Here the charge of the oxygens is spread on both of then. As is also the charge on the DMPC-phosphate oxygens? How can it then be a distance between atoms, when the charge is spread over several atoms? The program identifies the interacting charge groups within the cutoff specified, and then prints the minimum distance between any two atoms in the interacting charge groups, as stated in the thread you quote. Ah, now I understand the comment. Slow Friday. Thank you! -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 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
SV: SV: [gmx-users] g_saltbr
Sarah Witzke wrote: Dear gmx users, I'm sorry to continue an old thread - here's a summary: I have a DMPC bilayer surrounded by water and a small organic molecule with a deprotonated carboxylic acid. The small molecule diffuses near the membrane interface/into the membrane. I would like to calculate any formed salt bridge between the negative carboxylic acid of the small molecule and the positive charge of the DMPC choline nitrogen. To do this I use these two commands: g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 10 g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 10 -sep The first command I use to get the files min-min.xvg, plus-plus.xvg and plus-min.xvg. Here I am interested in plus-min.xvg to tell me which of the salt bridges between the small molecule and DMPC is between the negative acid and the positive choline (as opposed to between the negative acid and the negative phosphate of DMPC). Then I run the command again with -sep to get the individual graphs of each interaction. This is unfortunately a rather tedious exercise since very many files are generated for all sort of charged interactions (DMPC-DMPC, smallmolecule-smallmolecule, counterion-counterion, and pairs thereof), and then I have to select the wanted ones by looking through plus-min.xvg. I guess I could make some sort of script to make it easier, but I just want to check if there is absolutely no way to include an .ndx file or only choose plus-min interactions? Per the documentation, the only options that can be passed to g_saltbr are -s and -f, so no, you cannot use any index groups. I thought so :-( Another thing, when running the second command several of each files are generated, for instance: sb-DMPC144:DMPC154.xvg #sb-DMPC144:DMPC154.xvg.3# Etc The files are not identical when checked with diff or looked at in xmgrace. I suppose the last generated files are the correct one, but what are all the other files? Previous attempts at running the command generate backups. These sb-*.xvg files only come from using the -sep option, so issuing only the two commands above would not generate any backups (the ones that are flanked by #). Have you run different g_saltbr commands in the same directory? Perhaps using different values of -b and/or -t? There are no old xvg files in the directory. I have used rm -rf *xvg* to clean up and checked with ls -alt. Just now I also ran the command in a folder that I have not analyzed before - with the same huge amount og #-files. Also note the dates of the files are within minutes, eg.: -rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 sb-DMPC191:DMPC192.xvg -rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.1# -rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.2# -rw-r--r-- 1 sawit02 users 699 2009-12-02 00:56 #sb-DMPC191:DMPC192.xvg.3# -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 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] g_saltbr
Dear gromacs users, First of all thank you for all your previous help! I have a new question regarding an analysis of ionic interactions between DMPC lipids and a small molecule with a deprotonated carboxylic acid. g_saltbr takes as input an .xtc file and a .tpr file and from these files it measures the distance between all charged groups and create the three files min-min.xgv, plus-plus.xvg and min-plus.xvg. My bilayer contains 128 DMPC molecules each having a positively charge and a negative charge. The small molecule has one negative charge. Running g_saltbr -f xxx.xtc -s xxx.tpr -sep -b 10 -t 0.5 puts the distances between charged atoms in separate files, which is what I would like. But now the files are named like this: sb-small molecule'number':DMPC'number'.xvg How can I then know whether the small molecule is interacting with a positive atom in DMPC (like plus-min) or a negative atom in DMPC (like min-min)? One more question is on the distance: From this mail I read that the distance calculated is between the charged atoms, not the COM of the charge group: http://lists.gromacs.org/pipermail/gmx-users/2005-June/015811.html Then what about my small molecule with the deprotonated acid? Here the charge of the oxygens is spread on both of then. As is also the charge on the DMPC-phosphate oxygens? How can it then be a distance between atoms, when the charge is spread over several atoms? Thank you, Sarah -- 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_saltbr
-Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Fri 20-11-2009 14:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_saltbr Sarah Witzke wrote: Dear gromacs users, First of all thank you for all your previous help! I have a new question regarding an analysis of ionic interactions between DMPC lipids and a small molecule with a deprotonated carboxylic acid. g_saltbr takes as input an .xtc file and a .tpr file and from these files it measures the distance between all charged groups and create the three files min-min.xgv, plus-plus.xvg and min-plus.xvg. My bilayer contains 128 DMPC molecules each having a positively charge and a negative charge. The small molecule has one negative charge. Running g_saltbr -f xxx.xtc -s xxx.tpr -sep -b 10 -t 0.5 puts the distances between charged atoms in separate files, which is what I would like. But now the files are named like this: sb-small molecule'number':DMPC'number'.xvg How can I then know whether the small molecule is interacting with a positive atom in DMPC (like plus-min) or a negative atom in DMPC (like min-min)? If you omit the -sep option, you'll get plus-min.xvg, min-min.xvg, and plus-plus.xvg. In these, you will find the different groups that interact through these different charge interactions. OK. One more question is on the distance: From this mail I read that the distance calculated is between the charged atoms, not the COM of the charge group: http://lists.gromacs.org/pipermail/gmx-users/2005-June/015811.html Then what about my small molecule with the deprotonated acid? Here the charge of the oxygens is spread on both of then. As is also the charge on the DMPC-phosphate oxygens? How can it then be a distance between atoms, when the charge is spread over several atoms? The program identifies the interacting charge groups within the cutoff specified, and then prints the minimum distance between any two atoms in the interacting charge groups, as stated in the thread you quote. Ah, now I understand the comment. Slow Friday. Thank you! -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 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: SV: SV: SV: [gmx-users] Hydrogen bonding
-Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Thu 19-11-2009 02:09 To: Gromacs Users' List Subject: Re: SV: SV: SV: [gmx-users] Hydrogen bonding Sarah Witzke wrote: Sarah Witzke wrote: snip ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per hbond is 628.571 ps? Yes, per the calculation. For a bit more about the analysis, see the Please read and cite notices, as well as this thread: http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html The note about the correlation function would imply that the correlation function itself has not converged until its value is 0.001. This is usually a result of insufficient data, either the length of the simulation, or number of frames analyzed (based on the spacing of the frames). Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps) is not long enough. Perhabs I should try the original .trr file... The .xtc file I'm using only contains DMPC and the small molecule, no solvent - I can't see this would make a difference in this case, am I right? The correlation will depend on how much the interactions are changing over the period you analyzed. If you are analyzing a small molecule and DMPC, water should not matter. I have now tried with the full length (220 ns) .trr file and the -ac output still prints a warning: ACF 106/106 Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.000172327 +/- 0.00277407 In your opinion, does this mean that I cannot trust the value of the lifetime, since the correlation function is not converging? I'm not entirely sure. Please see the posts from David in the thread I referenced before about some potential issues with the ACF in the g_hbond calculation. I assume you are using version 4.0.x? I'm using version 4.0.4 for consistency. I have read the posts from you and David van der Spoel (http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html) as well as the article given by g_hbond. I guess this auto correlation function and the lifetime derived by this is... well, I'm not sure I trust it enough to put it in a paper - especially since my acf doesn't converge (which I still find strange, it should not matter that I have only saved coordinates every 10 ps in my .trr file when using the Luzar acfs-approached, right?). The - hbm option i g_hbond creates a matrix that can be converted to a .eps file by usin xpm2ps. The picture obtained is nice looking but lacking in some of the information I would like to derive. I would like to know how many frames each hbond exists (another way to consider lifetime). I have opened the .xpm file in a text editor and there are a long list of lines starting similar to tgis one: /* x-axis: 10 100010 100020 Can I somehow obtain the number of frames for each hbond from this? Thank you very much again! -Justin Thank you! I have conducted the analysis on the -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 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
SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote:
Dear gmx-users,
I have done simulations of one small molecule that diffuses into a DMPC
membrane. This small molecule contains an alcohol group and is therefore
capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol
region).
I have read the manual (section 8.12 and g_hbond -h), searched the mailing
list and google but I have not been able to find a more thorough description
of the output possibilities than in the manual.
I have tried three different approaches:
1. The -OH group of the small molecule and the glycerol oxygens
2. The -OH group of the small molecule and the phosphate oxygens
3. The small molecule and DMPC (no subgroups)
No. 1 gives 38 hbond, no. 2 gives 15 hbonds and no. 3 gives 53 hbonds. So 1 +
2 = 3, which is fine.
I'm assuming this is just some theoretical limit that you have established, and
not something that has actually been calculated, correct?
This is from the output of the program, you have explained it below :-)
Below is the output from no. 1: (gromacs 4.0.4)
Specify 2 groups to analyze:
Selected 0: 'O11__PALC_H12__PALC'
Selected 1: 'O7__DMPC__DMPC_O9__DMPC_O10__DMPC'
Checking for overlap in atoms between O11__PALC_H12__PALC and
O7__DMPC__DMPC_O9__DMPC_O10__DMPC
Calculating hydrogen bonds between O11__PALC_H12__PALC (2 atoms) and
O7__DMPC__DMPC_O9__DMPC_O10__DMPC (384 atoms)
Found 1 donors and 385 acceptors
Making hbmap structure...done.
Will do grid-seach on 15x15x24 grid, rcut=0.35
Found 15 different hydrogen bonds in trajectory
Found 23 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 15 to 15
- Reduced number of distances from 23 to 23
Average number of hbonds per timeframe 0.083 out of 192.5 possible
What does these 15 different hydrogen bond in trajectory mean? I don't
understand this. I also don't understand Average number of hbonds per
That means quite literally what it says: there are 15 distinct hydrogen bonds
that form at some point in your trajectory. They are listed in hbond.ndx
(output of -hbn) and mapped in hbmap.xpm (from -hbm). You should find that
there are 15 :)
Yes, I see this. Do you by the way know why this .ndx files under the title [
donors_hydrogens_DMPC ] lists a lot of non-heteroatoms (carbon atoms)?
timeframe 0.083 out of 192.5 possible - 192.5 possible hbonds?? Can anyone
shed some light on this?
You have 385 H-bond acceptors (see the output above). It appears that g_hbond
makes a simple assumption that if half of these were occupied (with the other
half of the group serving as a donor, which may or may not ever have any
physical significance), then the maximum number of H-bonds would be 385/2 =
192.5.
The average printed is simply the average number of H-bonds that are present
between your two groups at any given time. If your small molecule has only one
-OH group that you're considering, the maximum number of H-bonds per timeframe
is 1.
Ok.
Another question relates to the lifetime of the hbond calculated when the
-life flag is given. The produced .xvg file contain three columns: time,
p(t), and t p(t). What is p(t) and t p(t)? And how can I find the lifetime?
The explanation is probably in one of the Please read and cite the following
reference messages that g_hbond spits out. Looks like some sort of probability
function. You should also be cautioned by this warning from using the -life
option:
Note that the lifetime obtained in this manner is close to useless
Use the -ac option instead and check the Forward lifetime
When I use the -ac option I get this output:
...
ACF 53/53
Normalization for c(t) = 1.19876 for gh(t) = 9.96115e-05
WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) 0.001
Tail value (average C(t) over second half of acf): 0.0155651 +/- 0.014574
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 5.76828e-05
Q = 0
--
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.001682.571 20.705 5.76828e-05
Backward0.013 75.432 15.245
One-way 0.001 1001.338 21.655
Integral0.000 3419.839 24.700
Relaxation 0.001 1216.745 22.138
100%
...
When looking at the produced .xvg file I see these three data sets as a
function of time:
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
In neither the output nor the .xvg file I see any mention of 'Forward
lifetime'. Perhabs this is because of the warning 'Correlation function is
probably not long enough because the standard deviation in the tail of C(t)
0.001' which I sadly don't understand. Is this a matter of actual length of the
.xtc file? I use
SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote:
snip
Yes, I see this. Do you by the way know why this .ndx files under the title [
donors_hydrogens_DMPC ] lists a lot of non-heteroatoms (carbon atoms)?
No clue. Probably the code identifies the functional group to which the donor
belongs. The more pertinent directive is the [ hbonds... ] one, which contains
the indices of the atoms actually participating in hydrogen bonding.
snip
When I use the -ac option I get this output:
...
ACF 53/53
Normalization for c(t) = 1.19876 for gh(t) = 9.96115e-05
WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) 0.001
Tail value (average C(t) over second half of acf): 0.0155651 +/- 0.014574
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 5.76828e-05
Q = 0
--
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.001682.571 20.705 5.76828e-05
Backward0.013 75.432 15.245
One-way 0.001 1001.338 21.655
Integral0.000 3419.839 24.700
Relaxation 0.001 1216.745 22.138
100%
...
When looking at the produced .xvg file I see these three data sets as a
function of time:
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
In neither the output nor the .xvg file I see any mention of 'Forward
lifetime'. Perhabs this is because of the warning 'Correlation function is
probably not long enough because the standard deviation in the tail of C(t)
0.001' which I sadly don't understand. Is this a matter of actual length of
the .xtc file? I use the last 120 ns of a 220 ns simulation. Any suggestions?
Please see the following output line:
Forward 0.001682.571 20.705 5.76828e-05
ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per
hbond is 628.571 ps?
The note about the correlation function would imply that the correlation
function itself has not converged until its value is 0.001. This is usually a
result of insufficient data, either the length of the simulation, or number of
frames analyzed (based on the spacing of the frames).
Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps)
is not long enough. Perhabs I should try the original .trr file... The .xtc
file I'm using only contains DMPC and the small molecule, no solvent - I can't
see this would make a difference in this case, am I right?
Thank you,
Sarah
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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SV: SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote: snip ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per hbond is 628.571 ps? Yes, per the calculation. For a bit more about the analysis, see the Please read and cite notices, as well as this thread: http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html The note about the correlation function would imply that the correlation function itself has not converged until its value is 0.001. This is usually a result of insufficient data, either the length of the simulation, or number of frames analyzed (based on the spacing of the frames). Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps) is not long enough. Perhabs I should try the original .trr file... The .xtc file I'm using only contains DMPC and the small molecule, no solvent - I can't see this would make a difference in this case, am I right? The correlation will depend on how much the interactions are changing over the period you analyzed. If you are analyzing a small molecule and DMPC, water should not matter. I have now tried with the full length (220 ns) .trr file and the -ac output still prints a warning: ACF 106/106 Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.000172327 +/- 0.00277407 In your opinion, does this mean that I cannot trust the value of the lifetime, since the correlation function is not converging? Thank you! I have conducted the analysis on the -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 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] Hydrogen bonding
Dear gmx-users, I have done simulations of one small molecule that diffuses into a DMPC membrane. This small molecule contains an alcohol group and is therefore capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol region). I have read the manual (section 8.12 and g_hbond -h), searched the mailing list and google but I have not been able to find a more thorough description of the output possibilities than in the manual. I have tried three different approaches: 1. The -OH group of the small molecule and the glycerol oxygens 2. The -OH group of the small molecule and the phosphate oxygens 3. The small molecule and DMPC (no subgroups) No. 1 gives 38 hbond, no. 2 gives 15 hbonds and no. 3 gives 53 hbonds. So 1 + 2 = 3, which is fine. Below is the output from no. 1: (gromacs 4.0.4) Specify 2 groups to analyze: Selected 0: 'O11__PALC_H12__PALC' Selected 1: 'O7__DMPC__DMPC_O9__DMPC_O10__DMPC' Checking for overlap in atoms between O11__PALC_H12__PALC and O7__DMPC__DMPC_O9__DMPC_O10__DMPC Calculating hydrogen bonds between O11__PALC_H12__PALC (2 atoms) and O7__DMPC__DMPC_O9__DMPC_O10__DMPC (384 atoms) Found 1 donors and 385 acceptors Making hbmap structure...done. Will do grid-seach on 15x15x24 grid, rcut=0.35 Found 15 different hydrogen bonds in trajectory Found 23 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped - Reduced number of hbonds from 15 to 15 - Reduced number of distances from 23 to 23 Average number of hbonds per timeframe 0.083 out of 192.5 possible What does these 15 different hydrogen bond in trajectory mean? I don't understand this. I also don't understand Average number of hbonds per timeframe 0.083 out of 192.5 possible - 192.5 possible hbonds?? Can anyone shed some light on this? Another question relates to the lifetime of the hbond calculated when the -life flag is given. The produced .xvg file contain three columns: time, p(t), and t p(t). What is p(t) and t p(t)? And how can I find the lifetime? Thank you in advance, Sarah -- 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] g_bundle to calculate angle with z-axis
Dear gromacs users, I am conducting an analysis on my system consisting of a DMPC bilayer with small organic molecules inserting into it. The small molecule consists of a ring with two substituents opposite each other (like para for a benzene ring). Below I have tried to sketch the ring of the molecule with the two 'para' substituents: 2 | / \ | | \ / | 1 I want to create a vector starting in '1' and having the arrow head in '2' and then calculate how the angle between this vector and the z-axis varies during the simulation. To do this I created an .ndx file consisting of two groups, namely the atom '1' and the atom '2'. Afterwards I used g_bundle (version 4.0.4 since my simulations are done in this version): g_bundle -f xxx.xtc -s xxx.tpr -n xxx.ndx -na 1 -z -ot xxx.xvg When asked for two groups I first give group 0 corresponding to atom '1' and the I give group 1 corresponding to atom '2'. The result is rotated 180 degrees from what I would expect from looking at the simulation. Am I giving the groups in the wrong order? Will the order used correspond to a vector starting in '2' and with arrow head in '1'? By the way, is 1 the correct value for -na in this situation? I find it a bit difficult to understand that paragraph of the manual. Thank you, Sarah -- 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
SV: [gmx-users] g_bundle to calculate angle with z-axis
By the way, I did try to choose the groups in the opposite order - i.e. first select atom '2' and then '1'. The result is a reflection in the bilayer plane - and thereby the expected result. I just wanted to be sure, that what I am doing is correct, and that it is not just coincidence that swopping the groups gives the 'wanted' result. To me it seems logic that the vector created would start in the first selected atom and have the arrow head in the second atom, but perhaps I'm just wrong ;-) By the way the structure of the molecule should have looked like this: 2 | / \ | | \ / | 1 Best, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Sarah Witzke Sendt: sø 08-11-2009 20:49 Til: Discussion list for GROMACS users Emne: [gmx-users] g_bundle to calculate angle with z-axis Dear gromacs users, I am conducting an analysis on my system consisting of a DMPC bilayer with small organic molecules inserting into it. The small molecule consists of a ring with two substituents opposite each other (like para for a benzene ring). Below I have tried to sketch the ring of the molecule with the two 'para' substituents: 2 | / \ | | \ / | 1 I want to create a vector starting in '1' and having the arrow head in '2' and then calculate how the angle between this vector and the z-axis varies during the simulation. To do this I created an .ndx file consisting of two groups, namely the atom '1' and the atom '2'. Afterwards I used g_bundle (version 4.0.4 since my simulations are done in this version): g_bundle -f xxx.xtc -s xxx.tpr -n xxx.ndx -na 1 -z -ot xxx.xvg When asked for two groups I first give group 0 corresponding to atom '1' and the I give group 1 corresponding to atom '2'. The result is rotated 180 degrees from what I would expect from looking at the simulation. Am I giving the groups in the wrong order? Will the order used correspond to a vector starting in '2' and with arrow head in '1'? By the way, is 1 the correct value for -na in this situation? I find it a bit difficult to understand that paragraph of the manual. Thank you, Sarah -- 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
RE: [gmx-users] Z-position calculation
Hi, To get the z coordinate of the center of mass of a molecule I use the following command: echo number of molecule | g_traj -f xxx.xtc -s xxx.tpr -n xxx.ndx -nox -noy -com -ox xxx.xvg I guess you can create an .ndx file for a lipid head group to get the z coordinate of this. Regards, Sarah -Original Message- From: gmx-users-boun...@gromacs.org on behalf of TJ Piggot Sent: Tue 06-10-2009 11:55 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Z-position calculation Hi, You could also try g_bundle -z, it might do what you want. Cheers Tom --On Tuesday, October 06, 2009 11:04:29 +0200 XAvier Periole x.peri...@rug.nl wrote: g_traj with an index and playing with the different options. On Oct 6, 2009, at 11:01 AM, Moutusi Manna wrote: Dear all, I want to calculate the vertical position (Z-axis) of different lipid head groups as a function of time. Looking forward for any suggestion. Thanks in advance, Moutusi Manna __ Now, send attachments up to 25MB with Yahoo! India Mail. Learn how.___ 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 -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ 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
SV: [gmx-users] Error message: Cut-off length is longer than halfthe shortest box vector
Which version of gromacs are you using? If you are using version 4.0 editconf will change your box dimensions to zero. Fra: gmx-users-boun...@gromacs.org på vegne af Mark Abraham Sendt: ti 29-09-2009 05:48 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] Error message: Cut-off length is longer than halfthe shortest box vector Lum Nforbi wrote: Hello everyone, Thanks to Tsjerk, Mark Abraham, Justin and Dr. Vitaly for the very useful inputs to my quest for generating a .gro file from a .pdb file. I am now trying to minimize the energy of the system so I can do an mdrun but I keep having 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. I have changed the values of rlist, rvdw and rcoulomb, Don't, unless you know what you're doing. Your force field is parametrized under certain conditions, and varying these quantities by much will remove you from conditions where the force field might be supposed to work well. It does sound like you would benefit from doing some general background reading about molecular mechanics force fields and molecular dynamics simulations, and/or some more tutorial material. and even the box size several times but I still keep having this message. Please, You can change your box size with editconf, and then you will need to use genconf (or other) to increase the amount of solvent. I need help to figure out what to do to fix this problem. The command line I am using is:grompp -f waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr This command generates a (binary) run input file. It does not do anything to the box size, which it reads from the -c file. Also, is there a way to convert atom types from one format to another? I also have the following warnings: Warning: atom name 1 in water.top and waters_b.gro does not match (OW - O) Warning: atom name 2 in water.top and waters_b.gro does not match (HW1 - H) Warning: atom name 3 in water.top and waters_b.gro does not match (HW2 - H) atom names from water.top will be used atom names from waters_b.gro will be ignored. I had drawn my molecule in ghemical and exported as a pdb file and so the atom types O and H were automatically generated. Using the coordinate file output from pdb2gmx for subsequent operations is the correct way to avoid these warnings. If you're not using pdb2gmx then you need to really understand what you're doing. 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 ___ 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
SV: [gmx-users] diffusion coefficient with g_msd
Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mode= Linear This should be fine, right? I have indeed removed the overall COM motion for each step of the simulation? Just to be sure: To convert the .trr file to an .xtc I could use this command: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc I should not use -center (is that redundant when having nstcomm and comm_mode in the .mdp file?) or -fit rot+trans? Would your advice be to use -pbc nojump or just not -pbc at all? One last question: What is really the difference between -pbc nojumb and whole? I looked at g_msd -h for version 4.0.2, 4.0.3, and 4.0.4 (I'm using 4.0.4) and they all had the -rmcomm option, the manual version 3.3 doesn't mention it however. Thank you, Sarah #.mdp file# title= DMPC-LIM bilayer, 1 LIM and 128 lipids cpp = /lib/cpp integrator = md dt = 0.002 ; ps tinit= 0 init_step= 5000 nsteps = 7500 ;- ; Bond constraints define =; posres etc. constraints = all-bonds ; constrain all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default ; X/V/F/E outputs nstxout = 5000 ; pos out --- 10 ps nstvout = 5000 ; vel out --- 10 ps nstfout = 0 ; force out --- no ;nstlog = 5000 ; energies to log (0.5 ps) nstenergy= 5000 ; energies to energy gile ; Neighbour list ns_type = grid ; neighlist type nstlist = 10; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range NL) ; Coulomb interactions coulombtype = PME ; Particle Mesh Ewald rcoulomb = 1.0 ; nm (direct space sum cut-off) optimize_fft = yes ; optimal FFT plan for the grid ; van der Waals interactions vdwtype = Cut-off ; Van der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) ; Temperature coupling Tcoupl = berendsen tc-grps = DMPC LIM_SOL tau_t = 0.1 0.1; ps ref_t = 310 310; K ; Energy monitoring energygrps = DMPC LIM_SOL ; Pressure coupling Pcoupl = berendsen Pcoupltype = semiisotropic; semi: (xy) and (z) separately tau_p = 1.0 1.0 ; ps compressibility = 4.5e-5 4.5e-5 ; 1/bar (water @ 1 atm, 300 K) ref_p = 1.0 1.0 ; bar # Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 09:34 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual pages) that g_msd uses the Einstein relation. Reading Molecular Modelling: principles and applications 2.ed. by Andrew Leach it is explained that the for calculating the diffusion coefficient the mean-squared distances should not be limited by the edges of the periodic box. In other words, we require a set of positions that have not been translated back into the central simulation cell. This makes sense since I try to calculate the distance a molecule diffuse. I haven't been able to find any mention of how gromacs handle this either in the manual or on the wiki page. The search function on the old webpage directs me to the new webpage, which doesn't give any results for g_msd or diffusion coefficient or alike, so my apologies for asking a question I could have found the answer to I old emails. When I google I get some of the old emails on g_msd from the gromacs website, but I can only read some of them (the others direct me to an empty page in the new webpage). The first question is whether I can use my .xtc file made with this command from the original .trr file: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc (for fitting
SV: SV: [gmx-users] diffusion coefficient with g_msd
Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mode= Linear For bilayer systems it is often recommended to removed the solvent and bilayer separately, they may move in opposite directions and also you remove the COM of the system the solvent and bilayer might move on relative to the other. Thank you very much for telling me that. I'm sorry to ask, but how can you can you remove motion for the bilayer separately from the solvent? This should be fine, right? I have indeed removed the overall COM motion for each step of the simulation? Just to be sure: To convert the .trr file to an .xtc I could use this command: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc I should not use -center (is that redundant when having nstcomm and comm_mode in the .mdp file?) or -fit rot+trans? Would your advice be to use -pbc nojump or just not -pbc at all? One last question: What is really the difference between -pbc nojumb and whole? No, you just feed g_msd the trajectory trr the way it is. Or convert it in xtc if you like. You have to monitor the COM of the bilayer to check that the COM is indeed removed. For this you can do: 1) trjconv -f traj.trr -pbc nojump -o traj-nojump.xtc 2) g_traj -f traj-nojump.xtc -com -ox coord-COM.xvg -n index.ndx; in that step you choose the bilayer in your index and get the coordinates of the COM for which you can monitor the x, y and z values. Oh, I'm sorry to have written my last email to fast, I meant to erase -center, -fit, and -pbc from the command :-( I'll try your suggestions with trjconv and g_traj. I looked at g_msd -h for version 4.0.2, 4.0.3, and 4.0.4 (I'm using 4.0.4) and they all had the -rmcomm option, the manual version 3.3 doesn't mention it however. I was referring to the versions prior 4.0.X. It might be good to use it, it is definitely necessary to remove it. Thank you, Sarah #.mdp file# title= DMPC-LIM bilayer, 1 LIM and 128 lipids cpp = /lib/cpp integrator = md dt = 0.002 ; ps tinit= 0 init_step= 5000 nsteps = 7500 ;- ; Bond constraints define =; posres etc. constraints = all-bonds ; constrain all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default ; X/V/F/E outputs nstxout = 5000 ; pos out --- 10 ps nstvout = 5000 ; vel out --- 10 ps nstfout = 0 ; force out --- no ;nstlog = 5000 ; energies to log (0.5 ps) nstenergy= 5000 ; energies to energy gile ; Neighbour list ns_type = grid ; neighlist type nstlist = 10; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range NL) ; Coulomb interactions coulombtype = PME ; Particle Mesh Ewald rcoulomb = 1.0 ; nm (direct space sum cut-off) optimize_fft = yes ; optimal FFT plan for the grid ; van der Waals interactions vdwtype = Cut-off ; Van der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) ; Temperature coupling Tcoupl = berendsen tc-grps = DMPC LIM_SOL tau_t = 0.1 0.1; ps ref_t = 310 310; K ; Energy monitoring energygrps = DMPC LIM_SOL ; Pressure coupling Pcoupl = berendsen Pcoupltype = semiisotropic; semi: (xy) and (z) separately tau_p = 1.0 1.0 ; ps compressibility = 4.5e-5 4.5e-5 ; 1/bar (water @ 1 atm, 300 K) ref_p = 1.0 1.0 ; bar # Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 09:34 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate
[gmx-users] diffusion coefficient with g_msd
Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual pages) that g_msd uses the Einstein relation. Reading Molecular Modelling: principles and applications 2.ed. by Andrew Leach it is explained that the for calculating the diffusion coefficient the mean-squared distances should not be limited by the edges of the periodic box. In other words, we require a set of positions that have not been translated back into the central simulation cell. This makes sense since I try to calculate the distance a molecule diffuse. I haven't been able to find any mention of how gromacs handle this either in the manual or on the wiki page. The search function on the old webpage directs me to the new webpage, which doesn't give any results for g_msd or diffusion coefficient or alike, so my apologies for asking a question I could have found the answer to I old emails. When I google I get some of the old emails on g_msd from the gromacs website, but I can only read some of them (the others direct me to an empty page in the new webpage). The first question is whether I can use my .xtc file made with this command from the original .trr file: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc (for fitting and centring the DMPC group is used) I would guess I could not, but should I then do the command again creating a new .xtc file, but without using -center and -pbc whole? My second question is why g_msd has the option -rmcomm to remove COM motion? How is g_msd created so that the diffusion coefficient can be calculated if COM motion is removed? Thank you very much for your time, Sarah ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
FW: [gmx-users] One more broken .trr file
Dear gromacs users, First, Justin, thank you for your reply! Second, I have a question regarding how to use a checkpoint file to rerun my broken .trr file (dmpclim1-870.trr). As I previously described my I have divided my simulation into smaller simulations, each of 200 ps duration. I did that in order not to loose too much data if the simulation should crash. I have further divided my simulations into five folders - each folder consists of a little over 200 small .trr files (and the corresponding .gro, .log, .gro, .tpr, and .out files to each of theses small .trr files) - this division is because of a limit of max. 200 hours simulation time per job on the cluster I'm using. Each time the 200 hours have been used, a new folder is created from where the simulation is continued. In each of these five folder I only found these two .cpt files: state.cpt and state_prev.cpt. My commands are: tpbconv -f dmpclim1-XX.trr -s dmpclim1-XX.tpr -e dmpclim1-XX.edr -extend 200 dmpclim1-YY.tpr mdrun_mpi -np 4 -v -s dmpclim1-YY.tpr -o dmpclim1-YY.trr -c dmpclim1-YY.gro -e dmpclim1-YY.edr -g dmpclim1-YY.log dmpclim1-YY.out I guess that since a new checkpoint file is written every 15 minutes that it will overwrite the previous one. Is that correct? It seems unfortunate to me that it does not make new .cpt files for each small .trr file as it is done for e.g. .log files (naming them something like #state.cpt.1# and so on). If I have understood it correctly I'm not able to use my checkpoint file, because my simulation continued without errors thus overwriting the needed .cpt files several times. To learn from my mistakes: Next time I do simulations will an option like -cpo dmpclim1-YY.cpt create a checkpoint file for each small .trr file? Best, Sarah -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Sat 21-03-2009 13:20 To: Discussion list for GROMACS users Subject: Re: [gmx-users] One more broken .trr file Sarah Witzke wrote: Dear gromacs users, I would very much appreciate it if anyone could give me an advice on the following situation: I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files each of ~0.2 ns (giving a total of 1098 small .trr files). There were no errors or otherwise suspicious behavior during the simulation. After the simulation I concatenated all the small .trr files into one big .trr file (version 4.0.2 to correspond with other simulations): trjcat -f *.trr -o dmpclim1-all.trr trjcat gave no error message, the last line output to the screen was: last frame written was 219600.015625 ps After the concatenation I checked the big .trr file with gmxcheck: gmxcheck -f dmpclim1-all.trr The result was: Checking file dmpclim1-all.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 35508 Reading frame 17000 time 17.016 Warning at frame 17379: coordinates for atom 10917 are large (-2.99061e+19) Warning at frame 17379: coordinates for atom 10921 are large (1.42767e+31) Warning at frame 17379: coordinates for atom 10925 are large (-1.29194e+13) Warning at frame 17379: coordinates for atom 10925 are large (1.51714e+34) Reading frame 21000 time 21.016 Item#frames Timestep (ps) Step 2196110 Time 2196110 Lambda 2196110 Coords 2196110 Velocities 2196110 Forces 0 Box 2196110 Frame 17379 is located in the small .trr file number 870. .trr file 870 consists of 22 frames and the error is in frame 20. Looking at dmpclim1-870.trr in VMD reveals that two water molecules are far, far away (as noted by gmxcheck) in frame 20. Both in frame 19 and in frame 21 the two waters are placed nicely in the box. The dmpclim1-870.log and the screen output from 870 are both normal (i.e. they look similar to all the other steps), so my guess is that something happened during writing to file? I remember a similar problem posted very recently: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Reading these emails I understand that there is no way to delete just a single frame - is that correct? When posting links, right-click the frame and open it in a new window/tab. Then you will have the link that actually points to the message you found. This link is just the search page :) I have thought about two possible options for me now: 1) Use the suggestion given by Justin Lemkul in the email mentioned: trjconv -f dmpclim1-870.trr -b 0 -e 19 -o xxx.trr This is guess would make me loose 3 frames corresponding to (0.2 ns/22)*3 = 0.027 ns. It's not a problem to have 0.027 ns less of simulation, but will it affect later on when I concatenate the small .trr files, convert them to an .xtc file, and then use
[gmx-users] One more broken .trr file
Dear gromacs users, I would very much appreciate it if anyone could give me an advice on the following situation: I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files each of ~0.2 ns (giving a total of 1098 small .trr files). There were no errors or otherwise suspicious behavior during the simulation. After the simulation I concatenated all the small .trr files into one big .trr file (version 4.0.2 to correspond with other simulations): trjcat -f *.trr -o dmpclim1-all.trr trjcat gave no error message, the last line output to the screen was: last frame written was 219600.015625 ps After the concatenation I checked the big .trr file with gmxcheck: gmxcheck -f dmpclim1-all.trr The result was: Checking file dmpclim1-all.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 35508 Reading frame 17000 time 17.016 Warning at frame 17379: coordinates for atom 10917 are large (-2.99061e+19) Warning at frame 17379: coordinates for atom 10921 are large (1.42767e+31) Warning at frame 17379: coordinates for atom 10925 are large (-1.29194e+13) Warning at frame 17379: coordinates for atom 10925 are large (1.51714e+34) Reading frame 21000 time 21.016 Item#frames Timestep (ps) Step 2196110 Time 2196110 Lambda 2196110 Coords 2196110 Velocities 2196110 Forces 0 Box 2196110 Frame 17379 is located in the small .trr file number 870. .trr file 870 consists of 22 frames and the error is in frame 20. Looking at dmpclim1-870.trr in VMD reveals that two water molecules are far, far away (as noted by gmxcheck) in frame 20. Both in frame 19 and in frame 21 the two waters are placed nicely in the box. The dmpclim1-870.log and the screen output from 870 are both normal (i.e. they look similar to all the other steps), so my guess is that something happened during writing to file? I remember a similar problem posted very recently: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Reading these emails I understand that there is no way to delete just a single frame - is that correct? I have thought about two possible options for me now: 1) Use the suggestion given by Justin Lemkul in the email mentioned: trjconv -f dmpclim1-870.trr -b 0 -e 19 -o xxx.trr This is guess would make me loose 3 frames corresponding to (0.2 ns/22)*3 = 0.027 ns. It's not a problem to have 0.027 ns less of simulation, but will it affect later on when I concatenate the small .trr files, convert them to an .xtc file, and then use that to calculate e.g. area/lipid or membrane thickness? Will there be a time-mismatch? 2) Redo step 870. I'm able to redo step 870 quite easily, but what will then happen when I try to concatenate all the small .trr files? I fear that the old -870.trr wouldn't be exactly identical to the new -870.trr (due to round-off) and that this would make a mismatch with -871.trr? I'm very sorry to ask this kind of question again, but I hope you'll bear with me and have the patience to help me! Best regards, Sarah ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] One more broken .trr file
Dear gromacs users, I would very much appreciate it if anyone could give me an advice on the following situation: I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files each of ~0.2 ns (giving a total of 1098 small .trr files). There were no errors or otherwise suspicious behavior during the simulation. After the simulation I concatenated all the small .trr files into one big .trr file (version 4.0.2 to correspond with other simulations): trjcat -f *.trr -o dmpclim1-all.trr trjcat gave no error message, the last line output to the screen was: last frame written was 219600.015625 ps After the concatenation I checked the big .trr file with gmxcheck: gmxcheck -f dmpclim1-all.trr The result was: Checking file dmpclim1-all.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 35508 Reading frame 17000 time 17.016 Warning at frame 17379: coordinates for atom 10917 are large (-2.99061e+19) Warning at frame 17379: coordinates for atom 10921 are large (1.42767e+31) Warning at frame 17379: coordinates for atom 10925 are large (-1.29194e+13) Warning at frame 17379: coordinates for atom 10925 are large (1.51714e+34) Reading frame 21000 time 21.016 Item#frames Timestep (ps) Step 2196110 Time 2196110 Lambda 2196110 Coords 2196110 Velocities 2196110 Forces 0 Box 2196110 Frame 17379 is located in the small .trr file number 870. .trr file 870 consists of 22 frames and the error is in frame 20. Looking at dmpclim1-870.trr in VMD reveals that two water molecules are far, far away (as noted by gmxcheck) in frame 20. Both in frame 19 and in frame 21 the two waters are placed nicely in the box. The dmpclim1-870.log and the screen output from 870 are both normal (i.e. they look similar to all the other steps), so my guess is that something happened during writing to file? I remember a similar problem posted very recently: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Reading these emails I understand that there is no way to delete just a single frame - is that correct? I have thought about two possible options for me now: 1) Use the suggestion given by Justin Lemkul in the email mentioned: trjconv -f dmpclim1-870.trr -b 0 -e 19 -o xxx.trr This is guess would make me loose 3 frames corresponding to (0.2 ns/22)*3 = 0.027 ns. It's not a problem to have 0.027 ns less of simulation, but will it affect later on when I concatenate the small .trr files, convert them to an .xtc file, and then use that to calculate e.g. area/lipid or membrane thickness? Will there be a time-mismatch? 2) Redo step 870. I'm able to redo step 870 quite easily, but what will then happen when I try to concatenate all the small .trr files? I fear that the old -870.trr wouldn't be exactly identical to the new -870.trr (due to round-off) and that this would make a mismatch with -871.trr? I'm very sorry to ask this kind of question again, but I hope you'll bear with me and have the patience to help me! Best regards, Sarah ___ gmx-users mailing listgmx-users@gromacs.org http://www.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: SV: SV: SV: [gmx-users] g_order version 4.0.x
I have now made a new .ndx file as written in the wiki - and it works!!! :-) Thank you very much for your time Justin, I think what had confused my was the way the .ndx file was made in 3.3.3 and then the previous threads about the new way to make .ndx file in gromacs 4.0.x Anyway, I'm very happy now! Thanks again. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 09-03-2009 23:42 To: Gromacs Users' List Subject: Re: SV: SV: SV: [gmx-users] g_order version 4.0.x Justin A. Lemkul wrote: Sarah Witzke wrote: My .xtc file is 219.41 ns and therefor I thought to just use the last ~100 ns where my molecules have diffused into the membrane. I have just run g_order again whitout the -b option: the result is the same, no order parameters. My index file consists of just one big group. In that groups are the carbon atoms of the two lipid chains (and the two carbonyl carbons) for each of my 128 lipids. When running g_order it reads the .ndx file like this: That is your problem. You need individual groups for each distinct carbon along the chain. For an example for proper creation of these groups, see here: http://wiki.gromacs.org/index.php/make_ndx *Edit* I have gone ahead and created a g_order page. The information about how to create index groups seems to fit better there. Please refer to the new g_order page: http://wiki.gromacs.org/index.php/g_order -Justin -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.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://www.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
SV: SV: [gmx-users] g_order version 4.0.x
Dear Justin and others, I have now tried the exact same command g_order command with the exact same result: /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 This gives - again - the wanted file for the deuterium order parameters, dmpclim3_order_4.xvg, and also the non-requested for file order.xvg. Both files - again - contain no parameters: /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3 more dmpclim3_order_4.xvg # This file was created Mon Mar 9 21:45:17 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Deuterium order parameters @xaxis label Atom @yaxis label Scd @TYPE xy /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3 more order.xvg # This file was created Mon Mar 9 21:45:17 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 # # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Order tensor diagonal elements @xaxis label Atom @yaxis label S @TYPE xy This is driving me crazy. Clearly I must be doing something wrong since it is working for Justin - but what? If anyone has any suggestions they'll be much appreciated! Another thing: David van der Spoel asked me to file a bugzilla which I have done. After the email from Justin he wrote to me and asked whether version 4.0.4 was working for me. I wanted to write him back to answer him that I would try this today when I was back from holiday, but every time I tried to email him my email couldn't be delivered. Am I - again - doing something wrong, or do I have bad gromacs karma? Best regards and thank you, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Sarah Witzke Sendt: ti 03-03-2009 11:37 Til: jalem...@vt.edu; Discussion list for GROMACS users Emne: SV: SV: [gmx-users] g_order version 4.0.x Good idea, I'll try that when I get home next week. -Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: ma 02-03-2009 13:58 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Thank you David, I have filled a bugzilla. g_order works for me under version 4.0.4, perhaps try an upgrade? -Justin Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel Sendt: ma 02-03-2009 10:55 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Gromacs users, I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I still haven't received it myself. I'm sorry for the inconvenience it might cause. Sarah Dear Gromacs Users, I have simulated a lipid bilayer (128 DMPC molecules) with some small hydrophobic molecules. These small molecules go from the water into the bilayer and I now want to do some analysis to see, whether this has changed e.g. membrane thickness or the order of the lipid tails. I'm new to gromacs and this is my first try with analysis. For analysing the order of the lipid tales, I use g_order. The first index file I created consisted of 28 groups - one for each of the 14 carbons (including the carbonyl-C) in the two chains. The atoms in each of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so each of the 28 groups in the index file consist of 128 atoms (an entry in make_ndx would look like this a c15 r DMPC). Then I tried g_order version 4.0.2: g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg I'm asked to Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: and then all the 28 groups are listed. This was not what I had expected; I thought g_order calculated the order parameter for all the tail carbons at once. I tried just choosing group 0 to see what happened: Not much - as was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg. This I found strange since I hadn't asked for them, but then I found this bugzilla report: http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ (no. 264) After reading that I also tried to specify all carbons
SV: SV: SV: [gmx-users] g_order version 4.0.x
My .xtc file is 219.41 ns and therefor I thought to just use the last ~100 ns where my molecules have diffused into the membrane. I have just run g_order again whitout the -b option: the result is the same, no order parameters. My index file consists of just one big group. In that groups are the carbon atoms of the two lipid chains (and the two carbonyl carbons) for each of my 128 lipids. When running g_order it reads the .ndx file like this: /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_5.xvg :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 4.0.4 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org 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. :-) /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order (-: Option Filename Type Description -f dmpclim3-all.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n dmpc_order.ndx InputIndex file -s dmpclim3-1.tpr InputRun input file: tpr tpb tpa -o order.xvg Output xvgr/xmgr file -od dmpclim3_order_5.xvg Output xvgr/xmgr file -os sliced.xvg Output xvgr/xmgr file -Sg sg-ang.xvg Output, Opt. xvgr/xmgr file -Sksk-dist.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -b time 0 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]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -d enum z Direction of the normal on the membrane: z, x or y -sl int1 Calculate order parameter as function of boxlength, dividing the box in #nr slices. -[no]szonly bool no Only give Sz element of order tensor. (axis can be specified with -d) -[no]unsat bool no Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. Taking z axis as normal to the membrane Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Using following groups: Groupname: C15__DMPC_C17__DMPC_C18__DMPC_C19__DMPC_C20__DMPC_C21__DMPC_C22__DMPC_C23__DMPC_C24__DMPC_C25__DMPC_C26__DMPC_C27__DMPC_C28__DMPC_C29__DMPC_C32__DMPC_C34__DMPC_C35__DMPC_C36__DMPC_C37__DMPC_C38__DMPC_C39__DMPC_C40__DMPC_C41__DMPC_C42__DMPC_C43__DMPC_C44__DMPC_C45__DMPC_C46__DMPC First atomname: C15 First atomnr 44 Reading frame 0 time0.000 Number of elements in first group: 3584 Reading frame 21000 time 21.016 Read trajectory. Printing parameters to file Back Off! I just backed up order.xvg to ./#order.xvg.3# Thank you for your very quick reply! Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: ma 09-03-2009 22:38 Til: Discussion list for GROMACS users Emne: Re: SV: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Justin and others, I have now tried the exact same command g_order command with the exact same result: /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 10 How long is the trajectory? Does the command work if you don't use -b? Maybe a huge skip in time is causing problems, although I don't think it should. What is in your .ndx file? This gives - again - the wanted file for the deuterium order parameters, dmpclim3_order_4.xvg, and also the non-requested for file order.xvg. Right, order.xvg is generated by default, whether you specify it or not. -Justin Both files - again - contain no parameters: /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3 more dmpclim3_order_4.xvg # This file was created Mon Mar 9 21:45:17 2009 # by the following command: # /home/nat-mem-sw/sawit02/gromacs-4.0.4
SV: SV: [gmx-users] g_order version 4.0.x
Good idea, I'll try that when I get home next week. -Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: ma 02-03-2009 13:58 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Thank you David, I have filled a bugzilla. g_order works for me under version 4.0.4, perhaps try an upgrade? -Justin Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel Sendt: ma 02-03-2009 10:55 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Gromacs users, I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I still haven't received it myself. I'm sorry for the inconvenience it might cause. Sarah Dear Gromacs Users, I have simulated a lipid bilayer (128 DMPC molecules) with some small hydrophobic molecules. These small molecules go from the water into the bilayer and I now want to do some analysis to see, whether this has changed e.g. membrane thickness or the order of the lipid tails. I'm new to gromacs and this is my first try with analysis. For analysing the order of the lipid tales, I use g_order. The first index file I created consisted of 28 groups - one for each of the 14 carbons (including the carbonyl-C) in the two chains. The atoms in each of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so each of the 28 groups in the index file consist of 128 atoms (an entry in make_ndx would look like this a c15 r DMPC). Then I tried g_order version 4.0.2: g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg I'm asked to Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: and then all the 28 groups are listed. This was not what I had expected; I thought g_order calculated the order parameter for all the tail carbons at once. I tried just choosing group 0 to see what happened: Not much - as was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg. This I found strange since I hadn't asked for them, but then I found this bugzilla report: http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ (no. 264) After reading that I also tried to specify all carbons in one single group and then run g_order again: g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: Group 0 (C15__DMPC_C17__DMPC_C18__DMPC_C19__DMPC_C20__DMPC_C21__DMPC_C22__DMPC_C23__DMPC_C24__DMPC_C25__DMPC_C26__DMPC_C27__DMPC_C28__DMPC_C29__DMPC_C32__DMPC_C34__DMPC_C35__DMPC_C36__DMPC_C37__DMPC_C38__DMPC_C39__DMPC_C40__DMPC_C41__DMPC_C42__DMPC_C43__DMPC_C44__DMPC_C45__DMPC_C46__DMPC) has 3584 elements There is one group in the index Reading frame 0 time 10.008 Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1# Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1# Reading frame 11000 time 21.016 Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted deuterium order .xvg file. So, in the bugzilla report it also said that the problem had been fixed in the CVS. Unfortunately I don't know what this is, could anyone explain me please? I tried g_order version 4.0.3 (again with the index file with only one group): g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_3.xvg Taking z axis as normal to the membrane Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Using following groups: Groupname: C15__DMPC_C17__DMPC_C18__DMPC_C19__DMPC_C20__DMPC_C21__DMPC_C22__DMPC_C23__DMPC_C24__DMPC_C25__DMPC_C26__DMPC_C27__DMPC_C28__DMPC_C29__DMPC_C32__DMPC_C34__DMPC_C35__DMPC_C36__DMPC_C37__DMPC_C38__DMPC_C39__DMPC_C40__DMPC_C41__DMPC_C42__DMPC_C43__DMPC_C44__DMPC_C45__DMPC_C46__DMPC First atomname: C15 First atomnr 44 Reading frame 0 time 10.008 Number of elements in first group: 3584 Reading frame 11000 time 21.016 Read trajectory. Printing parameters to file Now two order files are generated: The wanted dmpclim3_order_3.xvg and also order.xvg which I didn't request for. (No sg-ang.xvg and sk-dist.xvg this time). Unfortunately neither of the obtained .xvg files contain any order parameters: dmpclim3_order_3.xvg: # This file was created Sat Feb 28 20:02:09 2009 # by the following command
SV: [gmx-users] g_order version 4.0.x
Thank you David, I have filled a bugzilla. Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel Sendt: ma 02-03-2009 10:55 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Gromacs users, I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I still haven't received it myself. I'm sorry for the inconvenience it might cause. Sarah Dear Gromacs Users, I have simulated a lipid bilayer (128 DMPC molecules) with some small hydrophobic molecules. These small molecules go from the water into the bilayer and I now want to do some analysis to see, whether this has changed e.g. membrane thickness or the order of the lipid tails. I'm new to gromacs and this is my first try with analysis. For analysing the order of the lipid tales, I use g_order. The first index file I created consisted of 28 groups - one for each of the 14 carbons (including the carbonyl-C) in the two chains. The atoms in each of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so each of the 28 groups in the index file consist of 128 atoms (an entry in make_ndx would look like this a c15 r DMPC). Then I tried g_order version 4.0.2: g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg I'm asked to Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: and then all the 28 groups are listed. This was not what I had expected; I thought g_order calculated the order parameter for all the tail carbons at once. I tried just choosing group 0 to see what happened: Not much - as was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg. This I found strange since I hadn't asked for them, but then I found this bugzilla report: http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ (no. 264) After reading that I also tried to specify all carbons in one single group and then run g_order again: g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: Group 0 (C15__DMPC_C17__DMPC_C18__DMPC_C19__DMPC_C20__DMPC_C21__DMPC_C22__DMPC_C23__DMPC_C24__DMPC_C25__DMPC_C26__DMPC_C27__DMPC_C28__DMPC_C29__DMPC_C32__DMPC_C34__DMPC_C35__DMPC_C36__DMPC_C37__DMPC_C38__DMPC_C39__DMPC_C40__DMPC_C41__DMPC_C42__DMPC_C43__DMPC_C44__DMPC_C45__DMPC_C46__DMPC) has 3584 elements There is one group in the index Reading frame 0 time 10.008 Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1# Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1# Reading frame 11000 time 21.016 Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted deuterium order .xvg file. So, in the bugzilla report it also said that the problem had been fixed in the CVS. Unfortunately I don't know what this is, could anyone explain me please? I tried g_order version 4.0.3 (again with the index file with only one group): g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_3.xvg Taking z axis as normal to the membrane Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Using following groups: Groupname: C15__DMPC_C17__DMPC_C18__DMPC_C19__DMPC_C20__DMPC_C21__DMPC_C22__DMPC_C23__DMPC_C24__DMPC_C25__DMPC_C26__DMPC_C27__DMPC_C28__DMPC_C29__DMPC_C32__DMPC_C34__DMPC_C35__DMPC_C36__DMPC_C37__DMPC_C38__DMPC_C39__DMPC_C40__DMPC_C41__DMPC_C42__DMPC_C43__DMPC_C44__DMPC_C45__DMPC_C46__DMPC First atomname: C15 First atomnr 44 Reading frame 0 time 10.008 Number of elements in first group: 3584 Reading frame 11000 time 21.016 Read trajectory. Printing parameters to file Now two order files are generated: The wanted dmpclim3_order_3.xvg and also order.xvg which I didn't request for. (No sg-ang.xvg and sk-dist.xvg this time). Unfortunately neither of the obtained .xvg files contain any order parameters: dmpclim3_order_3.xvg: # This file was created Sat Feb 28 20:02:09 2009 # by the following command: # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_3.xvg # # g_order is part of G R O M A C S: # # Great Red Oystrich Makes All Chemists Sane # @title Deuterium order parameters @xaxis label Atom @yaxis label Scd @TYPE xy order.xvg: # This file was created Sat Feb 28 20:02:09 2009
[gmx-users] g_order version 4.0.x
Dear Gromacs users, I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I still haven't received it myself. I'm sorry for the inconvenience it might cause. Sarah Dear Gromacs Users, I have simulated a lipid bilayer (128 DMPC molecules) with some small hydrophobic molecules. These small molecules go from the water into the bilayer and I now want to do some analysis to see, whether this has changed e.g. membrane thickness or the order of the lipid tails. I'm new to gromacs and this is my first try with analysis. For analysing the order of the lipid tales, I use g_order. The first index file I created consisted of 28 groups - one for each of the 14 carbons (including the carbonyl-C) in the two chains. The atoms in each of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so each of the 28 groups in the index file consist of 128 atoms (an entry in make_ndx would look like this a c15 r DMPC). Then I tried g_order version 4.0.2: g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg I'm asked to Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: and then all the 28 groups are listed. This was not what I had expected; I thought g_order calculated the order parameter for all the tail carbons at once. I tried just choosing group 0 to see what happened: Not much - as was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg. This I found strange since I hadn't asked for them, but then I found this bugzilla report: http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ (no. 264) After reading that I also tried to specify all carbons in one single group and then run g_order again: g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_2.xvg Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation: Group 0 (C15__DMPC_C17__DMPC_C18__DMPC_C19__DMPC_C20__DMPC_C21__DMPC_C22__DMPC_C23__DMPC_C24__DMPC_C25__DMPC_C26__DMPC_C27__DMPC_C28__DMPC_C29__DMPC_C32__DMPC_C34__DMPC_C35__DMPC_C36__DMPC_C37__DMPC_C38__DMPC_C39__DMPC_C40__DMPC_C41__DMPC_C42__DMPC_C43__DMPC_C44__DMPC_C45__DMPC_C46__DMPC) has 3584 elements There is one group in the index Reading frame 0 time 10.008 Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1# Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1# Reading frame 11000 time 21.016 Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted deuterium order .xvg file. So, in the bugzilla report it also said that the problem had been fixed in the CVS. Unfortunately I don't know what this is, could anyone explain me please? I tried g_order version 4.0.3 (again with the index file with only one group): g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_3.xvg Taking z axis as normal to the membrane Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) Using following groups: Groupname: C15__DMPC_C17__DMPC_C18__DMPC_C19__DMPC_C20__DMPC_C21__DMPC_C22__DMPC_C23__DMPC_C24__DMPC_C25__DMPC_C26__DMPC_C27__DMPC_C28__DMPC_C29__DMPC_C32__DMPC_C34__DMPC_C35__DMPC_C36__DMPC_C37__DMPC_C38__DMPC_C39__DMPC_C40__DMPC_C41__DMPC_C42__DMPC_C43__DMPC_C44__DMPC_C45__DMPC_C46__DMPC First atomname: C15 First atomnr 44 Reading frame 0 time 10.008 Number of elements in first group: 3584 Reading frame 11000 time 21.016 Read trajectory. Printing parameters to file Now two order files are generated: The wanted dmpclim3_order_3.xvg and also order.xvg which I didn't request for. (No sg-ang.xvg and sk-dist.xvg this time). Unfortunately neither of the obtained .xvg files contain any order parameters: dmpclim3_order_3.xvg: # This file was created Sat Feb 28 20:02:09 2009 # by the following command: # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_3.xvg # # g_order is part of G R O M A C S: # # Great Red Oystrich Makes All Chemists Sane # @title Deuterium order parameters @xaxis label Atom @yaxis label Scd @TYPE xy order.xvg: # This file was created Sat Feb 28 20:02:09 2009 # by the following command: # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 10 -od dmpclim3_order_3.xvg # # g_order is part of G R O M A C S: # # Great Red Oystrich Makes All Chemists Sane # @title Order tensor diagonal elements @xaxis label Atom @yaxis label S @TYPE xy I will be very thankful if anyone has any
SV: [gmx-users] Grompp error in 4.x regarding dihedral multiplicity
Hi again, Thank you very much for your reply Mark. Now, I have a dihedral with the following form: 22232425 1 0.0 7.471 22232425 1 0.0 3.9 2 22232425 1 180.0 1.1 3 22232425 1 0.0 -2.84250 Of course the problematic multiplicity of 0 just subtracts 5.685 from the energy. Would it then be OK to simply delete this line? I suppose it would be OK as it just adds a constant to the energy but I'm not 100% certain if it would give any problems with the calculation of forces. Sarah Sarah Witzke wrote: Dear gromacs users, I'm doing simulations of small molecules in lipid bilayers. Doing the simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But when I try to do an energy minimization of a POPC bilayer, grompp gives the following error: /people/disk2/sarah/gromacs-4.0.3/bin/grompp -f em.mdp -c system.gro -p popcpalc32.top -o test.tpr Ignoring obsolete mdp entry 'cpp' checking input for internal consistency... processing topology... Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxnb.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxbon.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ff_dum.itp Generated 1502 of the 2346 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1068 of the 2346 1-4 parameter combinations Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/flexspc.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/spc.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ions.itp Excluding 3 bonded neighbours molecule type 'PALC' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'POPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... --- Program grompp, VERSION 4.0.3 Source code file: convparm.c, line: 68 Fatal error: Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the minimum of 1 --- When looking through the lipid .itp file (popc.itp) I do see dihedrals with multiplicity of 0 (which is not the case in dmpc.itp) - I haven't made it myself but it has been used many times before. When running grompp in version 3.3.3 I get no error message: Yup - there was no test for validity of the input. Since a proper dihedral with multiplicity of zero is just a constant (see manual eq 4.61), it does nothing at all to the forces, nothing meaningful to energies and nothing to energy differences. Other than a convenient way to comment out dihedrals (which would be better done with a real comment!) I can't see the purpose of such dihedrals of multiplicity zero. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] Grompp error in 4.x regarding dihedral multiplicity
Dear gromacs users, I'm doing simulations of small molecules in lipid bilayers. Doing the simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But when I try to do an energy minimization of a POPC bilayer, grompp gives the following error: /people/disk2/sarah/gromacs-4.0.3/bin/grompp -f em.mdp -c system.gro -p popcpalc32.top -o test.tpr Ignoring obsolete mdp entry 'cpp' checking input for internal consistency... processing topology... Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxnb.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxbon.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ff_dum.itp Generated 1502 of the 2346 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1068 of the 2346 1-4 parameter combinations Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/flexspc.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/spc.itp Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ions.itp Excluding 3 bonded neighbours molecule type 'PALC' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'POPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... --- Program grompp, VERSION 4.0.3 Source code file: convparm.c, line: 68 Fatal error: Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the minimum of 1 --- When looking through the lipid .itp file (popc.itp) I do see dihedrals with multiplicity of 0 (which is not the case in dmpc.itp) - I haven't made it myself but it has been used many times before. When running grompp in version 3.3.3 I get no error message: /people/disk2/sarah/gromacs-3.3.3/bin/grompp -f em.mdp -c system.gro -p popcpalc32.top -o test.tpr creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 1502 of the 2346 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1068 of the 2346 1-4 parameter combinations Excluding 3 bonded neighbours for PALC 32 turning all bonds into constraints... Excluding 3 bonded neighbours for POPC 128 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 9800 turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # ANGLES: 17832 # PDIHS: 5152 # RBDIHS: 2688 # IDIHS: 608 # LJ14: 4288 # CONSTR: 26512 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /people/disk2/sarah/gromacs-3.3.3/share/top/aminoacids.dat There are: 9960 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... Making dummy/rest group for T-Coupling containing 36440 elements Making dummy/rest group for Acceleration containing 36440 elements Making dummy/rest group for Freeze containing 36440 elements Making dummy/rest group for Energy Mon. containing 36440 elements Making dummy/rest group for VCM containing 36440 elements Number of degrees of freedom in T-Coupling group rest is 82805.00 Making dummy/rest group for User1 containing 36440 elements Making dummy/rest group for User2 containing 36440 elements Making dummy/rest group for XTC containing 36440 elements Making dummy/rest group for Or. Res. Fit containing 36440 elements Making dummy/rest group for QMMM containing 36440 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... writing run input file... Does anyone have any suggestions? Thank you, Sarah ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
