Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
I got a fairly good number using fluctuations formula: cv=3.91J/K.g. I can't seem to figure out what am I doing wrong with g_energy. If someone could run /tutor/water/spc216 and get Cv it would be greatly appreciated. BTW, I do get interesting numbers for that system when I run g_energy -nmol 216 -ndf 9; Cv=55J/mol.K (close) g_energy -nmol 216 -ndf 10; Cv=88J/mol.K (even closer) Not that I can justify those ndf values though. F. On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > > Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is > > correct for ndf? I am running ffgmx force field and all bonds > > constrained spc water. > constrained SPC water has 6 dof (3x3 - 3 constraints). > > Is the temperature constant? > > Maybe you do not need the -nmol flag, otherwise it is time to check the > g_energy source code maybe. > > > F. > > > > > > On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > >> David, > >> I didn't realize what the nmol option does, thanks for the tip. But > >> the number went from 12.5 to 706.4 (I'm hiting my forehead on my desk > >> as I type this). BTW why ndf 6 and not 3? For rotation? > >> > >> On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > >>> Frankie Montenegro wrote: > OK but I thought your number comes from equipartition theorem, not > fluctuations. I think I remember correctly someone posting the code on > the list a while ago. > > Besides, I am also running 3000 SPC waters with Nose-Hoover. After > 250ps, the number is identical to the one from the example: 12.5 > J/mol.K > >>> did you use > >>> g_energy -nmol 3000 -ndf 6 ? > >>> > F. > > On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > > I am not sure what I'm missing here. I just ran an example from > > /tutor/water and got even worse > > number for specific heat, around 12.5 J/mol.K. Sure, it was with > > Berendsen T-coupling, no shifted VdW, but one would still expect > > better number. Anyone? > > Thanks, Frankie > > > ___ > 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 > > > -- > 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
Frankie Montenegro wrote: Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is correct for ndf? I am running ffgmx force field and all bonds constrained spc water. constrained SPC water has 6 dof (3x3 - 3 constraints). Is the temperature constant? Maybe you do not need the -nmol flag, otherwise it is time to check the g_energy source code maybe. F. On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: David, I didn't realize what the nmol option does, thanks for the tip. But the number went from 12.5 to 706.4 (I'm hiting my forehead on my desk as I type this). BTW why ndf 6 and not 3? For rotation? On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Frankie Montenegro wrote: OK but I thought your number comes from equipartition theorem, not fluctuations. I think I remember correctly someone posting the code on the list a while ago. Besides, I am also running 3000 SPC waters with Nose-Hoover. After 250ps, the number is identical to the one from the example: 12.5 J/mol.K did you use g_energy -nmol 3000 -ndf 6 ? F. On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: I am not sure what I'm missing here. I just ran an example from /tutor/water and got even worse number for specific heat, around 12.5 J/mol.K. Sure, it was with Berendsen T-coupling, no shifted VdW, but one would still expect better number. Anyone? Thanks, Frankie ___ 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 -- 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is correct for ndf? I am running ffgmx force field and all bonds constrained spc water. F. On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > David, > I didn't realize what the nmol option does, thanks for the tip. But > the number went from 12.5 to 706.4 (I'm hiting my forehead on my desk > as I type this). BTW why ndf 6 and not 3? For rotation? > > On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > Frankie Montenegro wrote: > > > OK but I thought your number comes from equipartition theorem, not > > > fluctuations. I think I remember correctly someone posting the code on > > > the list a while ago. > > > > > > Besides, I am also running 3000 SPC waters with Nose-Hoover. After > > > 250ps, the number is identical to the one from the example: 12.5 > > > J/mol.K > > > > did you use > > g_energy -nmol 3000 -ndf 6 ? > > > > > > > > F. > > > > > > On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > > >> I am not sure what I'm missing here. I just ran an example from > > >> /tutor/water and got even worse > > >> number for specific heat, around 12.5 J/mol.K. Sure, it was with > > >> Berendsen T-coupling, no shifted VdW, but one would still expect > > >> better number. Anyone? > > >> Thanks, Frankie > > >> > > > ___ > > > 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
David, I didn't realize what the nmol option does, thanks for the tip. But the number went from 12.5 to 706.4 (I'm hiting my forehead on my desk as I type this). BTW why ndf 6 and not 3? For rotation? On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > > OK but I thought your number comes from equipartition theorem, not > > fluctuations. I think I remember correctly someone posting the code on > > the list a while ago. > > > > Besides, I am also running 3000 SPC waters with Nose-Hoover. After > > 250ps, the number is identical to the one from the example: 12.5 > > J/mol.K > > did you use > g_energy -nmol 3000 -ndf 6 ? > > > > > F. > > > > On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > >> I am not sure what I'm missing here. I just ran an example from > >> /tutor/water and got even worse > >> number for specific heat, around 12.5 J/mol.K. Sure, it was with > >> Berendsen T-coupling, no shifted VdW, but one would still expect > >> better number. Anyone? > >> Thanks, Frankie > >> > > ___ > > 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
Frankie Montenegro wrote: OK but I thought your number comes from equipartition theorem, not fluctuations. I think I remember correctly someone posting the code on the list a while ago. Besides, I am also running 3000 SPC waters with Nose-Hoover. After 250ps, the number is identical to the one from the example: 12.5 J/mol.K did you use g_energy -nmol 3000 -ndf 6 ? F. On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: I am not sure what I'm missing here. I just ran an example from /tutor/water and got even worse number for specific heat, around 12.5 J/mol.K. Sure, it was with Berendsen T-coupling, no shifted VdW, but one would still expect better number. Anyone? Thanks, Frankie ___ 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
OK but I thought your number comes from equipartition theorem, not fluctuations. I think I remember correctly someone posting the code on the list a while ago. Besides, I am also running 3000 SPC waters with Nose-Hoover. After 250ps, the number is identical to the one from the example: 12.5 J/mol.K F. On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > I am not sure what I'm missing here. I just ran an example from > /tutor/water and got even worse > number for specific heat, around 12.5 J/mol.K. Sure, it was with > Berendsen T-coupling, no shifted VdW, but one would still expect > better number. Anyone? > Thanks, Frankie > ___ 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
Frankie Montenegro wrote: I am not sure what I'm missing here. I just ran an example from /tutor/water and got even worse number for specific heat, around 12.5 J/mol.K. Sure, it was with Berendsen T-coupling, no shifted VdW, but one would still expect better number. Anyone? Berendsen t coupling completely screws up the fluctuations. Not a chance to come even close. Thanks, Frankie ___ 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
I am not sure what I'm missing here. I just ran an example from /tutor/water and got even worse number for specific heat, around 12.5 J/mol.K. Sure, it was with Berendsen T-coupling, no shifted VdW, but one would still expect better number. Anyone? Thanks, Frankie ___ 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
On 9/11/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > > Hi again guys, > > > > Few more questions: > > > > 1. I would like to calculate compressibility of the protein+water > > system, but separating it into bulk water, hydration water and > > protein. So I need to pick these and compute volumes separately. When > > picking hydration water molecules, two tools are mentioned on the > > List: trjorder and g_hbond. Which one would you recommend for my task? > > Don't know, but I'd start by reading the man pages for each of those tools. > I did that. They both seem OK to me. I am not that experienced with Gromacs though, which is why I'm asking for suggestion. > > 2. a)The program g_energy gives output for compressibility. What > > method was used for that calculation? > > See the manual first. > Did that too. Didn't find anything. I suppose I could go through the code. > >b) When running g_energy I noticed a particularly crappy number for > > the specific heat of SPC water with ffgmx forcefield. It is about > > 17J/mol.K (should be about 75). > > I get similar number with my code using energy fluctuation method. > > Do you guys have any suggestions? I cut and paste my equilibration and > > production run mdp files. > > Why are you generating velocities post-equilibration? > Upps! Thanks. ___ 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
Frankie Montenegro wrote: On 9/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Frankie Montenegro wrote: That sounds difficult because computing volume is difficult. We should write a better program for this, but the problem lies in definition: where does one water molecule stop and the next begin? Thanks. I was hoping to use Voronoi volume for compressibility calculation. That should ensure that individual partial volumes add up to the complete volume. So, is any of the two (trjorder vs g_hbond) better? but neither of these programs calculate volumes. for selecting the nearest waters trjorder is easiest. This is because of Berendsen coupling. It should be better with Nose-Hoover or without (using shifted vdw potential as well). I suspected Berendsen coupling might be the problem. Should I expect anything close to the measured value with Nose-Hoover, but keeping vdw the way it is? I suggest you try both on pure water. Will take you half an hour. Regards, Frankie ___ 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
On 9/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > That sounds difficult because computing volume is difficult. We should > write a better program for this, but the problem lies in definition: > where does one water molecule stop and the next begin? > > > Thanks. I was hoping to use Voronoi volume for compressibility calculation. That should ensure that individual partial volumes add up to the complete volume. So, is any of the two (trjorder vs g_hbond) better? > This is because of Berendsen coupling. It should be better with > Nose-Hoover or without (using shifted vdw potential as well). I suspected Berendsen coupling might be the problem. Should I expect anything close to the measured value with Nose-Hoover, but keeping vdw the way it is? Regards, Frankie ___ 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
Frankie Montenegro wrote: Hi again guys, Few more questions: 1. I would like to calculate compressibility of the protein+water system, but separating it into bulk water, hydration water and protein. So I need to pick these and compute volumes separately. When picking hydration water molecules, two tools are mentioned on the List: trjorder and g_hbond. Which one would you recommend for my task? Don't know, but I'd start by reading the man pages for each of those tools. 2. a)The program g_energy gives output for compressibility. What method was used for that calculation? See the manual first. b) When running g_energy I noticed a particularly crappy number for the specific heat of SPC water with ffgmx forcefield. It is about 17J/mol.K (should be about 75). I get similar number with my code using energy fluctuation method. Do you guys have any suggestions? I cut and paste my equilibration and production run mdp files. Why are you generating velocities post-equilibration? 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] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
Frankie Montenegro wrote: Hi again guys, Few more questions: 1. I would like to calculate compressibility of the protein+water system, but separating it into bulk water, hydration water and protein. So I need to pick these and compute volumes separately. When picking hydration water molecules, two tools are mentioned on the List: trjorder and g_hbond. Which one would you recommend for my task? That sounds difficult because computing volume is difficult. We should write a better program for this, but the problem lies in definition: where does one water molecule stop and the next begin? 2. a)The program g_energy gives output for compressibility. What method was used for that calculation? b) When running g_energy I noticed a particularly crappy number for the specific heat of SPC water with ffgmx forcefield. It is about 17J/mol.K (should be about 75). This is because of Berendsen coupling. It should be better with Nose-Hoover or without (using shifted vdw potential as well). I get similar number with my code using energy fluctuation method. Do you guys have any suggestions? I cut and paste my equilibration and production run mdp files. Equilibration Thanks, Frankie cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md tinit = 0.0 dt = 0.001; ps ! nsteps = 1; total 10 ps. nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid comm-mode = Angular nstcomm = 1 comm-grps = System pbc = xyz coulombtype = PME rvdw= 0.9 rlist = 0.9 rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 275 ; Energy monitoring energygrps = System ; Pressure coupling is not on Pcoupl = no ; Random seed for Andersen thermostat andersen_seed= 815131 ; Generate velocites is on at 275 K. gen_vel = yes gen_temp= 275.0 gen_seed= 173529 NVT run cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.001; ps ! nsteps = 110 ; total 1.1ns. nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid comm-mode = Angular nstcomm = 1 comm-grps = System pbc = xyz coulombtype = PME rvdw= 0.9 rlist = 0.9 rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 275 ; Energy monitoring energygrps = System ; Pressure coupling is not on Pcoupl = no ; Generate velocites is on at 275 K. gen_vel = yes gen_temp= 275.0 gen_seed= 173529 ___ 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
