[gmx-users] Determining density of a gas in a simulation
Dear GROMACS Gurus, I wanted to determine the density of the ammonia gas in my simulation and compare this to the reference values and thought I could use g_density for this purpose. I recall being told that I need to perform a NPT simulation and achieve equilibrium. How do I perform an NPT simulation? I assume this means that I fix the number of molecules, the pressure, and the temperature. The number of molecules is definitely fixed and I define the temperature in my .mdp file through ref_t =240240. Is this the way in which to set the temperature in an NPT simulation? I do not currently specify any pressure in my simulation. Do I need to set the pressure as well through a ref_p setting? And does the ref_p setting simply need to satisfy the ideal gas equation for the specified N, T, V? And how do I determine when equilibrium is achieved? Should the potential energy of the system or some other value stabilize to within some deviation of the absolute value? If so, what would would be the acceptable limit of this deviation ... 5% of the value? Other percentage? Thanks. Darrell ___ 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] Determination of heat capacity of water
Does not mean it is correct... Please check the equations. It also depends on which T/P coupling you used. With Berendsen you will not obtain the correct answer. ... and why is that?? Thank you! Giulio ___ 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] Determining density of a gas in a simulation
Darrell Koskinen wrote: Dear GROMACS Gurus, I wanted to determine the density of the ammonia gas in my simulation and compare this to the reference values and thought I could use g_density for this purpose. I recall being told that I need to perform a NPT simulation and achieve equilibrium. How do I perform an NPT simulation? I assume this means that I fix the number of molecules, the pressure, and the temperature. The number of molecules is definitely fixed and I define the temperature in my .mdp file through ref_t =240240. Is this the way in which to set the temperature in an NPT simulation? I do not currently specify any pressure in my simulation. Do I need to set the pressure as well through a ref_p setting? And does the ref_p setting simply need to satisfy the ideal gas equation for the specified N, T, V? P and T can't be set. You can have an ensemble whose average over a long period has a value. You can use an algorithm to move them closer to a desired equilibrium value if the instantaneous one differs. See the manual for more information. Doing some tutorial material and some background reading sounds like a good idea, too. And how do I determine when equilibrium is achieved? Should the potential energy of the system or some other value stabilize to within some deviation of the absolute value? If so, what would would be the acceptable limit of this deviation ... 5% of the value? Other percentage? It depends - there's no hard-and-fast rule and it will vary with which observables you intend to measure. 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
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
So lets say that I delete the first frame from the trajectory in which some atoms might have been outside the box. Everything should be within the box once the simulation starts (from the second frame onwards)? So the procedure should work if the reference structure is the second frame? I have tried that, and it fails as well. On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole x.peri...@rug.nl wrote: The nojump option will not apply the pbc when an atom is crossing the box boundaries ... in your case your bilayer should definitely be in the center of your box and all the atoms in If not ot course it does not work! On Nov 5, 2009, at 4:33 PM, maria goranovic wrote: my starting structure looks quite all right to me. everything is in the box (except the tails of some lipids) .. wonder whats wrong. thank you verymuch for helping On Thu, Nov 5, 2009 at 4:04 PM, XAvier Periole x.peri...@rug.nl wrote: On Nov 5, 2009, at 4:00 PM, maria goranovic wrote: Hi Xavier, Thanks for the clear instructions. The bilayer is not in one piece in the z direction after the -pbc nojump for some reason. the problem might be from your starting structure, everything should be in the box! Or you may be facing strange/funny/incomprehensible behavior ... after the third step, the water is in the right place, but the bilayer has expanded to periodic boxes in the xy plane. so the center of mass of the lipid molecules is not really being centered in the box ? On Thu, Nov 5, 2009 at 3:34 PM, XAvier Periole x.peri...@rug.nl wrote: you need to do: 1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z direction 2- trjconv -center; using the bilayer to center and the system as output; this will translate your bilayer on the z axis and normally not modify it on the xy plan. 3- trjconv -pbc mol; will put your lipids in one piece in the box; I believe this step cn be coupled to the previous quite safely. On Nov 5, 2009, at 3:23 PM, maria goranovic wrote: One more note about -pbc nojump. I typically use -pbc mol. Using pbc nojump succeeds in keeping the center of the bilayer at 0 0 0, but the atoms have moved way out of the simulation box resulting in a dilute system On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic mariagorano...@gmail.com wrote: Centering on one atom has a problem that the lipid diffuses in the plane of the membrane, and as a result, the entire system starts to center around the lipid resulting in a simulation box which translates a lot in the bilayer plane. The splitting is not a problem, yes. But during the simulation period when the bilayer is not split, it diffuses quite a bit along the bilayer normal (after use of -pbc mol, and centering around the lipid center of mass). a plot of the lipid center of mass shows the bilayer diffusing along z, when its not split. On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole x.peri...@rug.nlwrote: On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote: maria goranovic wrote: I did use -pbc nojump, but that does not help What about entering on a central lipid tail atom, I suggested some time ago? The bilayer probably just splits across periodic boundaries, so this is not really a problem; just a visualization artefact. The splitting is not a problem and I think that centering using one lipid (tail) won't change the problem if the bilayer is cut half! Or the -pbc mol should be applied ... -Justin The drift is about 1 nm per 10 microseconds . (this is a martini simulation) On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole x.peri...@rug.nlmailto: x.peri...@rug.nl wrote: On Nov 5, 2009, at 12:09 PM, maria goranovic wrote: Hello All (and especially Berk) This is an update of the problem that I was facing earlier. I used to tau_p of 3.0 ps, and the problem does not go away, the bilayers still drifts in the simulation box. So this is probably a bug then? How much is the drift (nm/ns)? Did you use removal of center of mass of the entire system of bilayer/solvent separately? I still cannot understand how to put the bilayer back into the center of the simulation box. As suggested by Justin, I tried to use just one tail atom of a lipid for centering, but that did not work either. I noticed that my bilayer, which is initially at the center of the simulation box, separates into two leaflets at the box edges from the very first step of the simulation itself, but i am not able to correct that using the -center and -boxcenter zero options. Can someone please make a suggestion and help? You have to do use -pbc nojump first and then center ... Thank you so much -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
Lets make it clear. I can not tell you if the atoms in the second frame are in the box or not! You have to visualize it! Honestly it is not in the first frame I can not see how it would in the second! You have to build a reference structure that has the bilayer in one piece, then the nojump option can actually to the job you want. On Nov 6, 2009, at 10:37 AM, maria goranovic wrote: So lets say that I delete the first frame from the trajectory in which some atoms might have been outside the box. Everything should be within the box once the simulation starts (from the second frame onwards)? So the procedure should work if the reference structure is the second frame? I have tried that, and it fails as well. On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole x.peri...@rug.nl wrote: The nojump option will not apply the pbc when an atom is crossing the box boundaries ... in your case your bilayer should definitely be in the center of your box and all the atoms in If not ot course it does not work! On Nov 5, 2009, at 4:33 PM, maria goranovic wrote: my starting structure looks quite all right to me. everything is in the box (except the tails of some lipids) .. wonder whats wrong. thank you verymuch for helping On Thu, Nov 5, 2009 at 4:04 PM, XAvier Periole x.peri...@rug.nl wrote: On Nov 5, 2009, at 4:00 PM, maria goranovic wrote: Hi Xavier, Thanks for the clear instructions. The bilayer is not in one piece in the z direction after the -pbc nojump for some reason. the problem might be from your starting structure, everything should be in the box! Or you may be facing strange/funny/incomprehensible behavior ... after the third step, the water is in the right place, but the bilayer has expanded to periodic boxes in the xy plane. so the center of mass of the lipid molecules is not really being centered in the box ? On Thu, Nov 5, 2009 at 3:34 PM, XAvier Periole x.peri...@rug.nl wrote: you need to do: 1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z direction 2- trjconv -center; using the bilayer to center and the system as output; this will translate your bilayer on the z axis and normally not modify it on the xy plan. 3- trjconv -pbc mol; will put your lipids in one piece in the box; I believe this step cn be coupled to the previous quite safely. On Nov 5, 2009, at 3:23 PM, maria goranovic wrote: One more note about -pbc nojump. I typically use -pbc mol. Using pbc nojump succeeds in keeping the center of the bilayer at 0 0 0, but the atoms have moved way out of the simulation box resulting in a dilute system On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic mariagorano...@gmail.com wrote: Centering on one atom has a problem that the lipid diffuses in the plane of the membrane, and as a result, the entire system starts to center around the lipid resulting in a simulation box which translates a lot in the bilayer plane. The splitting is not a problem, yes. But during the simulation period when the bilayer is not split, it diffuses quite a bit along the bilayer normal (after use of -pbc mol, and centering around the lipid center of mass). a plot of the lipid center of mass shows the bilayer diffusing along z, when its not split. On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole x.peri...@rug.nl wrote: On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote: maria goranovic wrote: I did use -pbc nojump, but that does not help What about entering on a central lipid tail atom, I suggested some time ago? The bilayer probably just splits across periodic boundaries, so this is not really a problem; just a visualization artefact. The splitting is not a problem and I think that centering using one lipid (tail) won't change the problem if the bilayer is cut half! Or the -pbc mol should be applied ... -Justin The drift is about 1 nm per 10 microseconds . (this is a martini simulation) On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Nov 5, 2009, at 12:09 PM, maria goranovic wrote: Hello All (and especially Berk) This is an update of the problem that I was facing earlier. I used to tau_p of 3.0 ps, and the problem does not go away, the bilayers still drifts in the simulation box. So this is probably a bug then? How much is the drift (nm/ns)? Did you use removal of center of mass of the entire system of bilayer/solvent separately? I still cannot understand how to put the bilayer back into the center of the simulation box. As suggested by Justin, I tried to use just one tail atom of a lipid for centering, but that did not work either. I noticed that my bilayer, which is initially at the center of the simulation box, separates into two leaflets at the box edges from the very first step of the simulation itself, but i am not able to
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
For quite a long time I had the feeling that trjconv doesn't resolve all situations. Following the very recent discussion between Roland Schutz and Tsjerk, I'm not sure there is an immediate solution. Ad hoc approaches such as preparation of tpr files from intermediate snapshots were useful for me in some cases, so you can try these. For calculations of distances you can sometimes calculate the shift and apply an a posteriori fix, but that won't work for visualisation and isn't a robust solution. I don't think it has anything to do with the MARTINI FF. Ran. maria goranovic wrote: So lets say that I delete the first frame from the trajectory in which some atoms might have been outside the box. Everything should be within the box once the simulation starts (from the second frame onwards)? So the procedure should work if the reference structure is the second frame? I have tried that, and it fails as well. On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: The nojump option will not apply the pbc when an atom is crossing the box boundaries ... in your case your bilayer should definitely be in the center of your box and all the atoms in If not ot course it does not work! On Nov 5, 2009, at 4:33 PM, maria goranovic wrote: my starting structure looks quite all right to me. everything is in the box (except the tails of some lipids) .. wonder whats wrong. thank you verymuch for helping On Thu, Nov 5, 2009 at 4:04 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Nov 5, 2009, at 4:00 PM, maria goranovic wrote: Hi Xavier, Thanks for the clear instructions. The bilayer is not in one piece in the z direction after the -pbc nojump for some reason. the problem might be from your starting structure, everything should be in the box! Or you may be facing strange/funny/incomprehensible behavior ... after the third step, the water is in the right place, but the bilayer has expanded to periodic boxes in the xy plane. so the center of mass of the lipid molecules is not really being centered in the box ? On Thu, Nov 5, 2009 at 3:34 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: you need to do: 1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z direction 2- trjconv -center; using the bilayer to center and the system as output; this will translate your bilayer on the z axis and normally not modify it on the xy plan. 3- trjconv -pbc mol; will put your lipids in one piece in the box; I believe this step cn be coupled to the previous quite safely. On Nov 5, 2009, at 3:23 PM, maria goranovic wrote: One more note about -pbc nojump. I typically use -pbc mol. Using pbc nojump succeeds in keeping the center of the bilayer at 0 0 0, but the atoms have moved way out of the simulation box resulting in a dilute system On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic mariagorano...@gmail.com mailto:mariagorano...@gmail.com wrote: Centering on one atom has a problem that the lipid diffuses in the plane of the membrane, and as a result, the entire system starts to center around the lipid resulting in a simulation box which translates a lot in the bilayer plane. The splitting is not a problem, yes. But during the simulation period when the bilayer is not split, it diffuses quite a bit along the bilayer normal (after use of -pbc mol, and centering around the lipid center of mass). a plot of the lipid center of mass shows the bilayer diffusing along z, when its not split. On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote: maria goranovic wrote: I did use -pbc nojump, but that does not help What about entering on a central lipid tail atom, I suggested some time ago? The bilayer probably just splits across periodic boundaries, so this is not really a problem; just a visualization artefact. The splitting is not a problem and I think that centering using one lipid (tail) won't change
[gmx-users] empty edr and trr file
Hi, it seems to be solved with creating new configuration files, so sorry for bothering with it - however it never turned out what the problem was and why no complaints were written. Sorry again, ildiko ___ 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] Problem with simulation of aromatic structures in methanol
Respected Sir, I have problm with simulation of aromatic structures in methanol...the error which comes is like... checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Cleaning up temporary file gromppu2ZcH8 --- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive atomtypes, file methanol.itp, line 3 --- I have checked all the files...and the program runs fine for aliphatic structures Please tell me the point where i am making a mistake... With Regards Radhika The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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
