Re: [gmx-users] Fullerene simulation
Hi Serdar, The gromacs mailing list gives a hit on fullerene from earlier this year. Also, a quick search on scholar.google.com (http://scholar.google.nl/scholar?q=fullerene+gromacshl=enlr=btnG=Search) also gives some hits. Tsjerk On 8/31/07, serdar durdagi [EMAIL PROTECTED] wrote: Dear all, Is anybody studied with fullerene MD simulation using gromacs before? (I searched in literature, unfortunately I couldn't find). Best Wishes, Serdar Yahoo! Clever - Sie haben Fragen? Yahoo! Nutzer antworten Ihnen. ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Re: Measure contour area of bilayer undulation
Hi, On Aug 31, 2007, at 11:02 PM, Hwankyu Lee wrote: Thank you very much for your suggestion in the gromacs forum, but I may not understand your explanation completely. In the small bilayer, there is no fluctuation, so area/lipid can be calculated based on the cell dimensions. But, in the big bilayer, area/lipid can be much larger than that obtained from XYarea/lipid number because of undulations. First, try to keep the discussions on the list so the answers make it to the archive :-) Could you explain more details about reasons that area/lipid in the big bilayer can be calculated better based on cell dimensions? My point was rather the opposite - when people measure area/lipid in the lab on bilayer slabs there will be undulations present since they are typically not under tension. We discussed this with John Nagle a couple of years ago, and came to the conclusion that you should not try to compensate for it. This is one of the reasons you get more accurate results for larger systems. If you still want to derive it (the error is in the order of 1%, IIRC) you should start with the works of Nagle Safran! Cheers, Erik ___ 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] Fwd: what is the force function for proper dihedrals
[EMAIL PROTECTED] wrote:
Haven't looked into the details yet, but this is worth noting for those
interested. Thanks William.
- Forwarded message from [EMAIL PROTECTED] -
Date: Sat, 01 Sep 2007 00:15:25 -0400
From: William Noid [EMAIL PROTECTED]
Reply-To: William Noid [EMAIL PROTECTED]
Subject: what is the force function for proper dihedrals
To: [EMAIL PROTECTED]
howdy,
i am guessing that you want a formula for the cartesian force on the
atoms involved in a 4-body bonded interaction that is parameterized by a
dihedral angle. if so then all you have to do (of course) is to work
out a sort of nasty jacobian transforming the coordinates, but of course
it is kind of messy/cumbersome and easy to make a mistake. the only
published place i know where they have the answer explicitly is in the
dl_poly manual, which you can find at
http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/. they work it out in
gory detail on page 18 of the manual (which is actually page 30 of the
pdf file). i can't promise there are no typos there, but i think it is
quite likely correct. i have explicitly checked their calculation for
valence angles, though this is considerably easier. but at least this
would give you something to check against. one warning in advance: the
dl_poly folks define vectors in the opposite convention from normal.
see in the figure that r_ij is the vector from i to j - whereas i would
have defined r_ij as the vector from j to i.
anyway, i hope this is helpful. if this is what you wanted maybe you
could forward the info to the mailing list. if not, sorry to cause you
any bother.
there is a conference proceedings specifying how gromacs does it, which
is slightly more efficient than computing derivatives straight away.
looking at the title I get slightly uncertain. I have the book in my
office will have a look next week.
@inproceedings{Bekker93b,
author = {H. Bekker and H. J. C. Berendsen and E. J. Dijkstra
and S. Achterop and R. v. Drunen and D. v. d. Spoel and A. Sij\-bers and
H. Keegstra and B. Reitsma and M. K. R. Renardus},
title = {Gromacs Method of Virial Calculation Using a Single Sum},
booktitle = {Physics Computing 92},
pages = {257--261},
year = {1993},
editor = {R. A. de Groot and J. Nadrchal},
address = {Singapore},
publisher = {World Scientific},
}
--
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
___
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RE: [gmx-users] charge density of lipid
No, net charge density estimated from experimental data. Best regards Yuguang -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, September 01, 2007 4:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] charge density of lipid Mu Yuguang (Dr) wrote: Dear all, How to estimate the charge density of a lipid , the reason we want to do is that we try a model system to mimic the lipid environment. It seems out of GROMACS discussion range, but I believe many Gromacs users do lipid simulations. do you mean electron density? In that case there are plenty of tools in the CCP4 suite of programs. Best regards Yuguang ___ 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 ___ 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] charge density of lipid
I found one see this paper http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1302891blobtype=p df it is defined by sigma_M Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, September 01, 2007 4:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] charge density of lipid Mu Yuguang (Dr) wrote: No, net charge density estimated from experimental data. what does it mean, how is it measured? you can have nuclear charge minus electron density, but this is not very accurate. -- 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 ___ 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] r_list and r_coulomb values while using PME
Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advance Oz. ___ 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] r_list and r_coulomb values while using PME
OZGE ENGIN wrote: Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advance if rlist rcoulomb you will have a twin range interaction, meaning the atom pair interactions for distance between these two will be computed every nstlist steps only, while the interaction beyond rcoulomb will be computed at each time step. this will lead to bad energy conservation, since the force is not the derivative of the potential. Oz. ___ 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: Re: [gmx-users] r_list and r_coulomb values while using PME
'The force is not the derivative of the potential', is it due to the types of calculations performed in PME, using of FFT for reciprocal sum? Because it does not matter while using reaction-field method. Sorry, this phenomenon is a little complicated to me :) Thanks for your attention! Oz. -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 01 Sep 2007 13:37:05 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advance if rlist rcoulomb you will have a twin range interaction, meaning the atom pair interactions for distance between these two will be computed every nstlist steps only, while the interaction beyond rcoulomb will be computed at each time step. this will lead to bad energy conservation, since the force is not the derivative of the potential. Oz. ___ 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 ___ 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: Re: [gmx-users] r_list and r_coulomb values while using PME
So, using twin-range cut-off does not violate the energy conservation for RC method, but it violates for PME method. Is this the case ? -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 01 Sep 2007 14:48:03 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: 'The force is not the derivative of the potential', is it due to the types of calculations performed in PME, using of FFT for reciprocal sum? Because it does not matter while using reaction-field method. Sorry, this phenomenon is a little complicated to me :) this is only when you combine twin range (rcoulomb rlist) and PME. then the forces for a certain distance range are not computed at each time step while the others are. you may want to (re)read the PME papers and/or the gromacs manual about twin range. Thanks for your attention! Oz. -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 01 Sep 2007 13:37:05 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advance if rlist rcoulomb you will have a twin range interaction, meaning the atom pair interactions for distance between these two will be computed every nstlist steps only, while the interaction beyond rcoulomb will be computed at each time step. this will lead to bad energy conservation, since the force is not the derivative of the potential. Oz. ___ 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 ___ 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] r_list and r_coulomb values while using PME
OZGE ENGIN wrote: So, using twin-range cut-off does not violate the energy conservation for RC method, but it violates for PME method. Is this the case ? twin range does not conserve energy with cutoff or RF either. however you must always compromise between accuracy and computational cost, therefore in some cases twin range can be defended. -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 01 Sep 2007 14:48:03 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: 'The force is not the derivative of the potential', is it due to the types of calculations performed in PME, using of FFT for reciprocal sum? Because it does not matter while using reaction-field method. Sorry, this phenomenon is a little complicated to me :) this is only when you combine twin range (rcoulomb rlist) and PME. then the forces for a certain distance range are not computed at each time step while the others are. you may want to (re)read the PME papers and/or the gromacs manual about twin range. Thanks for your attention! Oz. -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 01 Sep 2007 13:37:05 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advance if rlist rcoulomb you will have a twin range interaction, meaning the atom pair interactions for distance between these two will be computed every nstlist steps only, while the interaction beyond rcoulomb will be computed at each time step. this will lead to bad energy conservation, since the force is not the derivative of the potential. Oz. ___ 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
