Re: [gmx-users] problem with undistribution of water
That problem is called periodic boundaries. Try inserting a second bilayer to get, at least on one axis, a water layer between the two lipid layers, if you want to prevent PBC for a part of the waters. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ sudheer babu wrote: Thanks Mr .Justin for your response, I am describing answers for your questions, 1.My box size is 6.0nm in xyz dimensions. 2.The forcefield I am using ffgmx.itp for membrane which I downloaded from Pieter Tieleman webiste and deprecated FF for protein. 3 .I inserted protein into membrane by using genbox command. 4. I used force constant 1 on protein. There is no leaking of membrane, the stucture is fine till EM, but in PR the water molecules are moving from one side of the bilyaer to the other side. No water mol between lipid bilyer hydrophobic region. Ok I tell you in clear way, Assume on membrane each side 200 water molecules are there but after equilabration 30 to 50 water molecules are reaching other side , so one side its appearing more rather than other side. But it looks in cubic form how appears in EM but only increasing water molecules on other side. Popc and protein are fine. Will it cause any problem later when I run further simulation by taking this output file.I hope you got my problem. Thanks in advance. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] query for g_sas
On Fri, 7 Mar 2008 00:42:46 +0530 (IST) Dilraj Lama [EMAIL PROTECTED] wrote: Hello gmx users, I suppose this is one of the more common subject post going around in the mailing list. I have gone through the list and have gathered some information on the subject. But I have some queries and if someone can shed light on it, it will be of great help to me. I am presently trying to calculate the sasa for specific residues as a function of time from my simulation trajectory.I am using g_sas tool from gromacs ver3.3 for the purpose.I wanted to check the values it generated. So I created a gly-X-gly tripeptide in an extended conformation and calculated the sasa for the twenty amino acids.I also calculated the same using the tool naccess.I then compared the two values with the value reported earlier for the various amino acids (J. Mol. Biol.196:641-656(1987)) Values for some of the amino acids are as: jmb Gromacs3.3 Naccess Ala 113 100 115 Arg 241 211 246 Asn 158 133 155 Asp 151 132 151 Cys 140 121 140 It seems the values from naccess and jmb(reported in J. Mol. Biol) are similar.I suppose one of the factor for the difference in values between naccess and gromacs3.3 could be because of the different VDW radii used for the atoms. Naccess uses Chothia's VDW radii whereas Gromacs3.3 uses the VDW radii as reported in gmx_sas.c. The difference you are seen is due to the use of different methods to measure the ASA. jmb and naccess use the Richards approach which is based on the surface defined by the center of a probe rolling on the vdW surface of the solute: the surface uses RvdW+Rsolvent. Gromacs is based on the Connolly surface which uses the vdW radius surface and connect them using a solvent probe: it uses the excluded volume from the solvent. The Connolly surface must be smaller as it does not include the radius of the probe in the calculation. Take a look at the links: http://www.msg.ucsf.edu/local/programs/moloc/surface.html http://www.netsci.org/Science/Compchem/feature14e.html XAvier Is it the case? Can I go ahead and perform the calculation using this tool? I have come accross papers which have used g_sas tool for performing the sasa calculation for the entire protein or peptide. Can anyone refer to me some papers where sasa calculation has been done for specific residues using g_sas. I have also read in the mailing list that differnet versions of Gromacs give different sasa values.people seem to report that values from Ver3.3, ver3.3.1 and ver3.3.2 are different. I haven't used 3.3.1 or 3.3.2. So what is the update in this front.Previous people who have gone through this, please help me out. Finally I also read in the list about the flexibility of chossing the VDW radii options. Has anything been done yet? Thank you. -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
Date: Thu, 6 Mar 2008 13:57:31 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling Berk Hess a écrit : Hi, I now realized that my fix what completely incorrect. I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5. But my mistake means that is now given an error when the off diagonal element is relatively more than 1 instead of more than 0.5. This is a far too weak check. So I would not expect any fatal errors any more with this incorrect check. Therefore I don't understand why you still get errors. Could you try changing BOX_MARGIN to 0.5005, as it currently is in version 4.0? Berk. We thus need a hot fix for 3.3.3? A too weak check does, by itself, not cause problems. It does mean that the check is useless, but Gromacs by itself never generates incorrect boxes. The problem with the check is still there, but it only seem to occur very rarely. I'll fix it properly in the CVS 3.3 patches branch. To Luther: Do you have by any hazard constraints= all-bonds if so, could you check if the run has the error with h-bonds? In my case that solved the issued with the error message. I suspect a rounding problem but i have not figured out it yet (not really searched for, btw). I don't think this should have anything to do with the problem directly. Indirectly it could help, but only when the system is unstable. Berk. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
Date: Fri, 7 Mar 2008 10:14:00 +0100
Date: Thu, 6 Mar 2008 13:57:31 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
Berk Hess a écrit :
Hi,
I now realized that my fix what completely incorrect.
I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5.
But my mistake means that is now given an error when the off diagonal
element is relatively more than 1 instead of more than 0.5.
This is a far too weak check.
So I would not expect any fatal errors any more with this incorrect check.
Therefore I don't understand why you still get errors.
Could you try changing BOX_MARGIN to 0.5005, as it currently is in
version 4.0?
Berk.
We thus need a hot fix for 3.3.3?
A too weak check does, by itself, not cause problems.
It does mean that the check is useless, but Gromacs
by itself never generates incorrect boxes.
The problem with the check is still there, but it only
seem to occur very rarely.
I'll fix it properly in the CVS 3.3 patches branch.
Hi Luther,
To be sure that this time I really fix the problem,
could you apply the following changes and check if the problem is gone?
Thanks,
Berk.
diff -r1.34.2.3 pbc.h
51,52c51,53
#define BOX_MARGIN 0.5001
/* margin factor for checking if the box is too skewed */
---
/* Margin factor for error message and correction if the box is too skewed */
#define BOX_MARGIN 0.5010
#define BOX_MARGIN_CORRECT 0.5005
diff -r1.57.2.9 pbc.c
100,102c100,102
else if ((fabs(box[YY][XX]) 2*BOX_MARGIN*box[XX][XX]) ||
(fabs(box[ZZ][XX]) 2*BOX_MARGIN*box[XX][XX]) ||
(fabs(box[ZZ][YY]) 2*BOX_MARGIN*box[YY][YY]))
---
else if ((fabs(box[YY][XX]) BOX_MARGIN*box[XX][XX]) ||
(fabs(box[ZZ][XX]) BOX_MARGIN*box[XX][XX]) ||
(fabs(box[ZZ][YY]) BOX_MARGIN*box[YY][YY]))
retrieving revision 1.84.2.8
diff -r1.84.2.8 ns.c
251c251
while (box[v][d] BOX_MARGIN*box[d][d]) {
---
while (box[v][d] BOX_MARGIN_CORRECT*box[d][d]) {
261c261
while (-box[v][d] BOX_MARGIN*box[d][d]) {
---
while (-box[v][d] BOX_MARGIN_CORRECT*box[d][d]) {
_
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RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions
Dave, -pbc mol did not work, however -pbc atom did. Also noted here: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Thank you. -Rob Date: Fri, 7 Mar 2008 07:42:41 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions rob yang wrote: Hi list, I have a system solvated in dodecahedron box. To visualize it, I used: trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole Version 3.3.3 gave me a cubic box with broken molecules while the previous versions gave me the right visualization on the same system.gro try -pbc mol. otherwsie you are welcome to submit a bugzilla. Does anybody have any similar experiences? Thanks. -Rob _ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions
rob yang wrote: Dave, -pbc mol did not work, however -pbc atom did. Also noted here: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Thank you. did not work is not good enough a description. However, the functionality has changed, intentionally. The -pbc atom breaks molecules and should be used with care (for visualization only). So hence I presume this is not a bug. -Rob Date: Fri, 7 Mar 2008 07:42:41 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions rob yang wrote: Hi list, I have a system solvated in dodecahedron box. To visualize it, I used: trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole Version 3.3.3 gave me a cubic box with broken molecules while the previous versions gave me the right visualization on the same system.gro try -pbc mol. otherwsie you are welcome to submit a bugzilla. Does anybody have any similar experiences? Thanks. -Rob _ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions
Dave, I am using it for visualization for now. -pbc mol gave me the same output as -pbc whole, which was a cubic box with broken protein. -pbc atom gave the dodecahedron box and intact protein. But since the functionality of -pbc mol has changed, and may not be applicable to visualization purposes, it is then not a bug. Judging from your reply, I seem to get the feeling that -pbc atom might not be a wise idea later on if I do actual analysis of the MD trajectory. Date: Fri, 7 Mar 2008 16:50:50 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions did not work is not good enough a description. However, the functionality has changed, intentionally. The -pbc atom breaks molecules and should be used with care (for visualization only). So hence I presume this is not a bug. _ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .gro files generation for a certain time-step interval in a simulation
Hi All, I wonder if anyone knows what is the command to use in order to generate .gro files for a certain time-step interval in a simulation? For example, if I have a completed simulation of 10 ns long and I want to output (somehow) 10 .gro files each at 1st ns, 2nd ns, 3rd ns and so on out from a series of output files that I have (.tpr, .xtc, .edr, .log). Do you think it's do-able? -- Best regards, Huey Ling ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions
rob yang wrote: Dave, I am using it for visualization for now. -pbc mol gave me the same output as -pbc whole, which was a cubic box with broken protein. -pbc atom gave the dodecahedron box and intact protein. But since the functionality of -pbc mol has changed, and may not be applicable to visualization purposes, it is then not a bug. Judging from your reply, I seem to get the feeling that -pbc atom might not be a wise idea later on if I do actual analysis of the MD trajectory. that is correct. but -pbc mol -ur compact should give you a dodecahedron but with intact molecules. If you have an example where -pbc mol gives you a broken molecule that is a bug, unless the protein was broken from the beginning, which it shouldn't be. If this is indeed the case then please submit a bugzilla. Date: Fri, 7 Mar 2008 16:50:50 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions did not work is not good enough a description. However, the functionality has changed, intentionally. The -pbc atom breaks molecules and should be used with care (for visualization only). So hence I presume this is not a bug. _ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions
Okay, my mistake. Here's what each option gave me (all with -ur compact): -pbc whole: broken protein, rectangular box -pbc mol: intact protein, rectangular box, part of protein sticking outside the box -pbc atom: intact protein, dodecahedron box but -pbc mol -ur compact should give you a dodecahedron but with intact molecules. Let me play around with it a little more before submitting the input files to bugzilla. Thank you. -Rob _ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] .gro files generation for a certain time-step interval in a simulation
trjconv -dump time Huey Ling Tan wrote: Hi All, I wonder if anyone knows what is the command to use in order to generate .gro files for a certain time-step interval in a simulation? For example, if I have a completed simulation of 10 ns long and I want to output (somehow) 10 .gro files each at 1st ns, 2nd ns, 3rd ns and so on out from a series of output files that I have (.tpr, .xtc, .edr, .log). Do you think it's do-able? -- Best regards, Huey Ling ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Position restraints on a lipid bilayer
Hello, I am looking to add position restraints to some atoms of a lipid bilayer. There seem to be a lot in the list archives on this subject, but I am still a tad confused. What I would like to do is to position restrain the phosphorus atoms in only one leaflet of the bilayer. So how do I generate such a pr file, and where should I include it? It seems as if things are done per molecule, so if I put it in my *.top or *.itp files, the restraint is on all P atoms in the system, not just the ones I want. Is there a way to do this so that things are indexed per atom rather than per molecule? Thanks, Mike ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Skewed box using Parrinello-Rahman pressure coupling
Hi Berk, I´ll try the setting you proposed and let you know wether it worked. Stephane, thanks for your tip but I already use h-bonds as the constraints option. Best Luther Berk Hess a écrit : Hi, I now realized that my fix what completely incorrect. I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5. But my mistake means that is now given an error when the off diagonal element is relatively more than 1 instead of more than 0.5. This is a far too weak check. So I would not expect any fatal errors any more with this incorrect check. Therefore I don't understand why you still get errors. Could you try changing BOX_MARGIN to 0.5005, as it currently is in version 4.0? Berk. We thus need a hot fix for 3.3.3? To Luther: Do you have by any hazard constraints= all-bonds if so, could you check if the run has the error with h-bonds? In my case that solved the issued with the error message. I suspect a rounding problem but i have not figured out it yet (not really searched for, btw). Cheers, Stéphane ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ED analysis, domain rotation, DynDom
Hi I have a done number of MD simulations of a two domain protein with different ligands and also in the apo state. Comparing these simulations I see varying degrees of domain rotation of the one domain relative to the other which I want to quantitatively measure and I was thinking of using DynDom to do this; I have already assessed a number of structures taken from different points throughout the simulations but want a to assess the motion throughout the simulations. From the user lists I read that I should do ED analysis first. Is this using g_covar and then g_anaeig or using make_edi and then doing ED in mdrun and then assessing these results? Also as the motion appears to be the C-terminal domain relative to the N-terminal domain when using g_covar should I fit over the N-terminal domain backbone but do the analysis over the whole backbone, or just fit over the whole backbone? Also in g_covar is it better for this type of problem to use the -ref option and assess the deviation from the conformation in the structure file instead of from the average? I would appreciate some guidance as although I've read some papers on this subject I am a bit confused as to what is the best way to progress. Many thanks, Jo. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Position restraints on a lipid bilayer
toma0052 wrote: Hello, I am looking to add position restraints to some atoms of a lipid bilayer. There seem to be a lot in the list archives on this subject, but I am still a tad confused. What I would like to do is to position restrain the phosphorus atoms in only one leaflet of the bilayer. So how do I generate such a pr file, and where should I include it? It seems as if things are done per molecule, so if I put it in my *.top or *.itp files, the restraint is on all P atoms in the system, not just the ones I want. Is there a way to do this so that things are indexed per atom rather than per molecule? Yep. Make two copies of the lipid molecule with the same parameters and different molecule names. Easiest to do this by copying an .itp file and changing names and stuff. Then you arrange to use a [ position_restraints ] field in one and not the other. If there's not already an #ifdef-ed [ position_restraints ] in your .itp file, then use an #ifdef like you get normally from pdb2gmx output, and change the #ifdef name in one of them so that you can selectively choose position restraints in one molecule type or the other. You can share one posre.itp file between both these sorts of lipid molecules, since the atomic index of P will be the same in both molecules. Then set up your bilayer such that the molecules in one leaflet precede the other leaflet. Now use the [ molecules ] section of your .top with suitable naming and ordering to permit yourself the ability to select P atoms in the various leaflets for PR. Chapter 5 will have more details on various aspects of the above. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Noive to gromacs : MD for zeolitic system
Dear Gromacs users, I would like to try Gromacs to conduct MD on my system which has, Zeolite( Ti,Si,O elements with pore and extraframework cations like Na+), water as solvent and some counterions in water. I am intrested to study the ionexcahnge in this system. I tried Dl_POLY but because of expensive CPU time, I am badly looking for another package which will help in fast computations.Any help and suggestions regarding this issue will be greatly appreciated. Thank you for your time in advance. Best Regards ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Noive to gromacs : MD for zeolitic system
anjaiah Nalaparaju wrote: Dear Gromacs users, I would like to try Gromacs to conduct MD on my system which has, Zeolite( Ti,Si,O elements with pore and extraframework cations like Na+), water as solvent and some counterions in water. I am intrested to study the ionexcahnge in this system. I tried Dl_POLY but because of expensive CPU time, I am badly looking for another package which will help in fast computations.Any help and suggestions regarding this issue will be greatly appreciated. If you don't already have access to a force field for your system formatted for use in GROMACS, then you'll have to write/convert your own. Extensive reference to Chapters 4 and 5 of the manual will be required. You should look around the web and literature for what might be available. It is worth doing some of the tutorial material to get a feel for how things fit together in GROMACS, even though they're mostly focussed on protein simulations. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error of moleculetype
Dear gromacs users, Hi, I have encounter the following error,after addition of Sodium ions to my system as it has -5.0 charge and before minimization. Fatal error: No such moleculetype Na I have checked errors of gromacs but I didn't understand that.Is I will write the word NA below the [moleculetype ] in topology file ? or some thing other work. Hoping for a favorable reply. Regards, SYED LAL BADSHAH M.Phil Scholar NCE in Physical Chemistry, University of Peshawar. NWFP,Pakistan. Cell # 03349060632. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error of moleculetype
s lal badshah wrote: Dear gromacs users, Hi, I have encounter the following error,after addition of Sodium ions to my system as it has -5.0 charge and before minimization. Fatal error: No such moleculetype Na I have checked errors of gromacs but I didn't understand that.Is I will write the word NA below the [moleculetype ] in topology file ? or some thing other work. See http://wiki.gromacs.org/index.php/Errors#Fatal_error:_No_such_moleculetype_XXX 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
