[gmx-users] Re: Density Deferences between spc216 and tip4p
Dear Jochen, Sorry to bother you. I did not calculate the densities it is the program output!. Is this a bug?. Regards Chandu Message: 8 Date: Thu, 13 Dec 2007 10:28:02 +0100 From: Jochen Hub [EMAIL PROTECTED] Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p water models To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed [EMAIL PROTECTED] wrote: Dear All, I was trying create a box (cubic 10 10 10) of water. I am a bit surprised by looking at the density deferences between spc216 and tip4p water models. I am giving the brief output below. genbox -cs tip4p.gro -box 10 10 10 Output configuration contains 131540 atoms in 32885 residues Volume :1000 (nm^3) Density: 1639.65 (g/l) Number of SOL molecules: 32885 Theres is something wrong in your calculation of the density. From 32885 Molcules (18g/mol) in a volume (10nm)^3 I get a density of 982 g/l. Cheers, Jochen genbox -cs spc2i6.gro -box 10 10 10 Output configuration contains 99678 atoms in 33226 residues Volume :1000 (nm^3) Density: 993.966 (g/l) Number of SOL molecules: 33226 What would be the reason for this drastic differences in density? How can I make it into 1000 (g/l) by using above command. Thanks in advance. Regards Chandu ___ 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 . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 44, Issue 37 * ___ 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] Re: Density Deferences between spc216 and tip4p
Chandu, It's clear you didn't do the calculations. Please do them yourself and see what answer you get for the density of 32885 water molecules in a box with volume 10^3 nm^3. Note also that there may be implicit assumptions underlying the value of the density provided by genbox, but it's the number of molecules that counts. Tsjerk On Dec 13, 2007 11:04 AM, [EMAIL PROTECTED] wrote: Dear Jochen, Sorry to bother you. I did not calculate the densities it is the program output!. Is this a bug?. Regards Chandu Message: 8 Date: Thu, 13 Dec 2007 10:28:02 +0100 From: Jochen Hub [EMAIL PROTECTED] Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p water models To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed [EMAIL PROTECTED] wrote: Dear All, I was trying create a box (cubic 10 10 10) of water. I am a bit surprised by looking at the density deferences between spc216 and tip4p water models. I am giving the brief output below. genbox -cs tip4p.gro -box 10 10 10 Output configuration contains 131540 atoms in 32885 residues Volume :1000 (nm^3) Density: 1639.65 (g/l) Number of SOL molecules: 32885 Theres is something wrong in your calculation of the density. From 32885 Molcules (18g/mol) in a volume (10nm)^3 I get a density of 982 g/l. Cheers, Jochen genbox -cs spc2i6.gro -box 10 10 10 Output configuration contains 99678 atoms in 33226 residues Volume :1000 (nm^3) Density: 993.966 (g/l) Number of SOL molecules: 33226 What would be the reason for this drastic differences in density? How can I make it into 1000 (g/l) by using above command. Thanks in advance. Regards Chandu ___ 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 . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 44, Issue 37 * ___ 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
Re: [gmx-users] trajectory concatenation
Hi all, I am doing some analysis with a 30 ns simulation of a 16 subunits protein. However, this simulation has two index files because of a stop in the middle of simulation, index file 1 for 0ns-20ns and index file 2 for 20ns-30ns. The same atoms in the two index files have different numbers. Now, I want to concatenate the trajectory of these two time intervals and i do not know how to do it. Could you give me some suggestions? Whatever procedure mapped atom i in the first simulation to atom j in the second simulation could now be applied to the values in the first index file. 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
Re: [gmx-users] Re: Density Deferences between spc216 and tip4p
[EMAIL PROTECTED] wrote: Dear Jochen, Sorry to bother you. I did not calculate the densities it is the program output!. Is this a bug?. Sorry to say that, but I don't have the feeling that it's my job to find the error in your calcuation... Regards Chandu Message: 8 Date: Thu, 13 Dec 2007 10:28:02 +0100 From: Jochen Hub [EMAIL PROTECTED] Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p water models To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed [EMAIL PROTECTED] wrote: Dear All, I was trying create a box (cubic 10 10 10) of water. I am a bit surprised by looking at the density deferences between spc216 and tip4p water models. I am giving the brief output below. genbox -cs tip4p.gro -box 10 10 10 Output configuration contains 131540 atoms in 32885 residues Volume :1000 (nm^3) Density: 1639.65 (g/l) Number of SOL molecules: 32885 Theres is something wrong in your calculation of the density. From 32885 Molcules (18g/mol) in a volume (10nm)^3 I get a density of 982 g/l. Cheers, Jochen genbox -cs spc2i6.gro -box 10 10 10 Output configuration contains 99678 atoms in 33226 residues Volume :1000 (nm^3) Density: 993.966 (g/l) Number of SOL molecules: 33226 What would be the reason for this drastic differences in density? How can I make it into 1000 (g/l) by using above command. Thanks in advance. Regards Chandu ___ 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 . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 44, Issue 37 * ___ 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 . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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] Re: Density Deferences between spc216 and tip4p
In TIP4P there is a fourth center (called M) close to the O atom. It reveals from the output that gromacs considers four atoms with this model but only three with SPC. If (this is a question) a mass is assigned to M in TIP4P, the density calculated by the PROGRAM must be larger than upon manual calculation and assuming 18 g for the molar mass of water Peter Nagy From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Thu 12/13/2007 5:04 AM To: gmx-users@gromacs.org Subject: [gmx-users] Re: Density Deferences between spc216 and tip4p Dear Jochen, Sorry to bother you. I did not calculate the densities it is the program output!. Is this a bug?. Regards Chandu Message: 8 Date: Thu, 13 Dec 2007 10:28:02 +0100 From: Jochen Hub [EMAIL PROTECTED] Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p water models To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed [EMAIL PROTECTED] wrote: Dear All, I was trying create a box (cubic 10 10 10) of water. I am a bit surprised by looking at the density deferences between spc216 and tip4p water models. I am giving the brief output below. genbox -cs tip4p.gro -box 10 10 10 Output configuration contains 131540 atoms in 32885 residues Volume :1000 (nm^3) Density: 1639.65 (g/l) Number of SOL molecules: 32885 Theres is something wrong in your calculation of the density. From 32885 Molcules (18g/mol) in a volume (10nm)^3 I get a density of 982 g/l. Cheers, Jochen genbox -cs spc2i6.gro -box 10 10 10 Output configuration contains 99678 atoms in 33226 residues Volume :1000 (nm^3) Density: 993.966 (g/l) Number of SOL molecules: 33226 What would be the reason for this drastic differences in density? How can I make it into 1000 (g/l) by using above command. Thanks in advance. Regards Chandu ___ 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 . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 44, Issue 37 * ___ 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] How to choose lipid molecules?
Dear all, I am a freshman to membrane protein simulation, and i was wondering how to choose lipid molecules for my system. As we know, there are lots of lipid molecules: DMPC, DPPC, POPE. but how do people decide that which type of lipid to use? and what kinds of criteria should we follow? Thanks so much! Liang___ 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] How to choose lipid molecules?
That depends entirely on the system you be simulating. In general you look at the type of membrane your system sits in and you try to match it with the lipids available. You also should look at the parameters that are available. Not all lipids are as good as they should. On Thu, 13 Dec 2007 22:48:16 +0800 liang [EMAIL PROTECTED] wrote: Dear all, I am a freshman to membrane protein simulation, and i was wondering how to choose lipid molecules for my system. As we know, there are lots of lipid molecules: DMPC, DPPC, POPE. but how do people decide that which type of lipid to use? and what kinds of criteria should we follow? Thanks so much! Liang - 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] How to choose lipid molecules?
liang wrote: Dear all, I am a freshman to membrane protein simulation, and i was wondering how to choose lipid molecules for my system. As we know, there are lots of lipid molecules: DMPC, DPPC, POPE. but how do people decide that which type of lipid to use? and what kinds of criteria should we follow? Lipids differ in their chain length, chain saturation, head groups size. There are, e.g., phospholipids, glycolipids. Some are ionic, zwitter-ionic, or neutral. They differ in the phases they adopt at whatever temperature, there are wedge-like and cone-like shapted lipids, etc. There are parameters for some lipids available (including those you mentioned), and for many there is no topology availabe (yet). Membranes may include glycerin, ... I guess you need to think abount the quetion you want to address and then choose the lipid you want to simulate. An important issue is, or course, to simulate a lipid membrane which you may compare to experiments. Cheers, Jochen Thanks so much! Liang ___ 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 -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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] Gel Phase in DMPC using Berger force field ??
Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist= 1.6 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.6 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 1.2 rvdw = 1.4 ** On 12/11/07, Eric Jakobsson [EMAIL PROTECTED] wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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 - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
I'm running MD at 300 K. I want fluid phase. On 12/13/07, Myunggi Yi [EMAIL PROTECTED] wrote: Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist= 1.6 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.6 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 1.2 rvdw = 1.4 ** On 12/11/07, Eric Jakobsson [EMAIL PROTECTED] wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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 - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing
[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
Dear users, I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (10684 water molecules) and a protein-water system. However, the average volume of the system that I get is from the simulations is different for the two versions. In case of pure water, gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is significantly higher than the fluctuations in the volume. The pressure is maintained at 1 bar and the temperature is maintained at 300 K using Berendsen barostat and thermostat respectively. I was wondering if someone could tell me why this happens? Has there been a modification in the pressure virial calculation or something related to the same that leads to these differences? Thank you Regards Sapna -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream ___ 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] Gel Phase in DMPC using Berger force field ??
What topology are you using? If you're using one based on the Kartunnen's group POPG (the only publicly available one I know of), then be aware that I think they saw gel phase too. Oh, and read the email you replied to, particularly the bit about 18 angstroms. - Original Message From: Myunggi Yi [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 13, 2007 6:48:20 PM Subject: Re: [gmx-users] Gel Phase in DMPC using Berger force field ?? I'm running MD at 300 K. I want fluid phase. On 12/13/07, Myunggi Yi [EMAIL PROTECTED] wrote: Dear Eric, I'm using Berger force field for DOPG (anionic head group). Is is true for DOPG also? The following is my MD input. I'm getting smaller area per lipid (~52 A^2) than expected (~62). What should I change? ** ; nblist cut-off rlist= 1.6 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.6 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 1.2 rvdw = 1.4 ** On 12/11/07, Eric Jakobsson [EMAIL PROTECTED] wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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
Re: [gmx-users] non-zero total charge for water
JMandumpal wrote: It says, System has non-zero total charge: -2.58e-01. [ molecules ] SOL 258 There's a pattern here. tip5P.itp file --- [ moleculetype ] ; molname nrexcl SOL2 [ atoms ] ; idat type res nr residu name at namecg nr charge #ifdef _FF_OPLS 1opls_1181SOL OW1 0 2opls_1191SOL HW11 0.24 3opls_1191SOL HW21 0.241 4opls_1201SOL LP11 -0.241 5opls_1201SOL LP21 -0.241 ... and there's a broken pattern here. 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] non-zero total charge for water
Dear Gromacs users, I built .tpr file prior to energy minimisation of box of tip5p water molecule. I received the output like this: calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 2 bonded neighbours for SOL 258 NOTE: System has non-zero total charge: -2.58e-01 processing coordinates... double-checking input for internal consistency... Cleaning up constraints and constant bonded interactions with virtual sites renumbering atomtypes... converting bonded parameters... # SETTLE: 258 # VSITE3OUT: 516 Setting particle type to V for virtual sites initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs/3.3.2-dp/share/gromacs/top/aminoacids.dat There are: 258 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... Making dummy/rest group for T-Coupling containing 1290 elements Making dummy/rest group for Acceleration containing 1290 elements Making dummy/rest group for Freeze containing 1290 elements Making dummy/rest group for Energy Mon. containing 1290 elements Making dummy/rest group for VCM containing 1290 elements Number of degrees of freedom in T-Coupling group rest is 1545.00 Making dummy/rest group for User1 containing 1290 elements Making dummy/rest group for User2 containing 1290 elements Making dummy/rest group for XTC containing 1290 elements Making dummy/rest group for Or. Res. Fit containing 1290 elements Making dummy/rest group for QMMM containing 1290 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... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 175x175x175, spacing 0.115 0.115 0.115 writing run input file... -- It says, System has non-zero total charge: -2.58e-01. What could be the problem. I tried to solve it, but I can't. what resulted the error? I paste my top and itp files below. sincerly, Jestin - topol.top #include ffoplsaa.itp #include tip5P.itp [ system ] Pure water [ molecules ] SOL 258 tip5P.itp file --- [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; idat type res nr residu name at namecg nr charge #ifdef _FF_OPLS 1 opls_1181SOL OW 1 0 2 opls_1191SOL HW11 0.24 3 opls_1191SOL HW21 0.241 4 opls_1201SOL LP11 -0.241 5 opls_1201SOL LP21 -0.241 [ settles ] ; i funct doh dhh 1 1 0.09572 0.15139 [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ;c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 | ; =20 ; ; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2) ; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31)
[gmx-users] g_hbond (v 3.14) vs g_hbond (3.3)
Dear Users, I have done clustering of equilibrium ensemble of octa-alanine model system, and when i was trying to find the no. of hydrogen bonds for each cluster, i found different result with different versions. Is there some bug to version 3.3 in comparison of version 3.14 or am i doing the wrong way. Please guide me. I have used the command g_hbond_mpi -f *.pdb -s *.tpr -num hbnum.xvg -hx hbhelix.xvg -r 0.35 -a 30 n-n n-n+1 n-n+2 n-n+3 n-n+4 n-n+5 n-n6 0 0 73 180 277 103618563422Cut-off r=0.35 a=30v3.14 0 0 330 243 358 138221704483Cut-off r=0.35 a=60v3.14 12252373404 0 0 0 0 4002Cut-off r=0.35 a=30v3.3 PS: In version 3.14 the default is r = 0.35 and a = 60 and in version 3.3 the default is r = 0.35 and a = 30 My worry is that when i did calculation with v 3.3 i got more no of n-n n-n+1 and n-n+2 hydrogen bonds, while on the same system with v 3.14 i found 0(Zero) value for n-n n-n+1 and n-n+2 (Quite Surprising with v3.3!) How come hydrogen bond between n-n is possible, when structures and everything is fine. Thanks in advance, With Regards Anil ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant ___ 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
