[gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility
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? 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). 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
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
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
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
[gmx-users] stopcom and acc_grps
Hi all， When I use acc_grps (e.g.: SOL), I think I should not use com motion removal on that group, even the whole system. Am I right? 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] stopcom and acc_grps
Zhou Bo wrote: Hi all， When I use acc_grps (e.g.: SOL), I think I should not use com motion removal on that group, even the whole system. Am I right? yes. 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 -- 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, 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
[gmx-users] Protein coming out of the box
Hi all I'm simulating a helical protein in a water box, neutralized with Na and Cl to a 0.2M comcentration. I had to pick the smallest box I could (in editconf, rectangular, with -d 0.1, and -princ to align the box with the helix). But in the MD trajectory I see the protein coming out of the box, most of the time. I know that it uses PBC, and I'm seeing just 1 image, but does it mean that there's something wrong with the MD? Thanks in advance, Gustavo This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ 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] Protein coming out of the box
[EMAIL PROTECTED] wrote: Hi all I'm simulating a helical protein in a water box, neutralized with Na and Cl to a 0.2M comcentration. I had to pick the smallest box I could (in editconf, rectangular, with -d 0.1, and -princ to align the box with the helix). But in the MD trajectory I see the protein coming out of the box, most of the time. I know that it uses PBC, and I'm seeing just 1 image, but does it mean that there's something wrong with the MD? http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions 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
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
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: 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
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
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] Help! A dummy atom definition problem!
The problem actually is, that you mixed up a dummy atom with a virtual site, I guess. Virtual sites are not allowed to have a mass, as the error message claims. Also, a proper hydrogen should have a mass. If you want a hydrogen to appear, you have to place a particle in A-state which has no non-bonded interaction, i.e. LJ QQ interactions should be zero. If you want to prevent it from flying away, you should put bonded terms to the particle. In the B-state, the QQ and LJ should be there (whereas the LJ interaction for a hydrogen is 0 anyway). 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 opls_999 DUM 0 1.008000 0.000A 0.00 0.00 So, I expect, this is, how it should look like. Be aware of the missing bonded terms in the force field for a DUM particle. Maybe, you want to call it H instead... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top, line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ 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
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] Help! A dummy atom definition problem!
Hi Maik, I really did mix up a dummy atom with a virtual site. Any difference? Thank you very much for your help. Regards, Qin On 9/12/07, Maik Goette [EMAIL PROTECTED] wrote: The problem actually is, that you mixed up a dummy atom with a virtual site, I guess. Virtual sites are not allowed to have a mass, as the error message claims. Also, a proper hydrogen should have a mass. If you want a hydrogen to appear, you have to place a particle in A-state which has no non-bonded interaction, i.e. LJ QQ interactions should be zero. If you want to prevent it from flying away, you should put bonded terms to the particle. In the B-state, the QQ and LJ should be there (whereas the LJ interaction for a hydrogen is 0 anyway). 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 opls_999 DUM 0 1.008000 0.000A 0.00 0.00 So, I expect, this is, how it should look like. Be aware of the missing bonded terms in the force field for a DUM particle. Maybe, you want to call it H instead... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top, line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ 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 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] Solaris x86 instalation problem
Hi, I'm instaling gromacs in a Sun x86 machine with Solaris 10. Configure seams to be ok but when compiling an error ocourrs. Could any one help me? Thanks the configure and compiling output: -bash-3.00$ ./configure checking build system type... i386-pc-solaris2.10 checking host system type... i386-pc-solaris2.10 checking for a BSD-compatible install... config/install-sh -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... nawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... plaintar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... no checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of cc... none checking how to run the C preprocessor... cc -E checking whether cc accepts -native -fast -xO5 -fsimple=2 -fnonstd -dalign... yes checking whether byte ordering is bigendian... no checking for egrep... egrep checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 4 checking for long long int... yes checking size of long long int... 8 checking floating-point format... configure: WARNING: Unknown floating-point format checking for a BSD-compatible install... config/install-sh -c checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for non-GNU ld... /usr/ucb/ld checking if the linker (/usr/ucb/ld) is GNU ld... no checking for /usr/ucb/ld option to reload object files... -r checking for BSD-compatible nm... /usr/ccs/bin/nm -p checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... CC checking whether we are using the GNU C++ compiler... no checking whether CC accepts -g... yes checking dependency style of CC... none checking how to run the C++ preprocessor... CC -E checking the maximum length of command line arguments... 262144 checking command to parse /usr/ccs/bin/nm -p output from cc object... ok checking for objdir... .libs checking for ar... false checking for ranlib... : checking for strip... : checking for cc option to produce PIC... -KPIC checking if cc PIC flag -KPIC works... yes checking if cc static flag -Bstatic works... no checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/ucb/ld) supports shared libraries... yes checking dynamic linker characteristics... solaris2.10 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... no checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag CXX to libtool checking whether the CC linker (/usr/ucb/ld) supports shared libraries... yes checking for CC option to produce PIC... -KPIC checking if CC PIC flag -KPIC works... yes checking if CC static flag -Bstatic works... no checking if CC supports -c -o file.o... yes checking whether the CC linker (/usr/ucb/ld) supports shared libraries... yes checking dynamic linker characteristics... solaris2.10 ld.so checking how to hardcode library paths into programs... immediate appending configuration tag F77 to libtool checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for _LARGE_FILES value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for fseeko... yes checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... yes checking rpc/rpc.h usability... yes checking rpc/rpc.h presence... yes checking for rpc/rpc.h... yes checking for rpc/xdr.h... yes checking for xdr_float in -lnsl... yes checking for working memcmp... yes checking return type of signal handlers... void checking for vprintf... yes checking for _doprnt... yes checking if malloc debugging is wanted... no checking for strcasecmp... yes checking for strdup... yes checking for bool... no checking for X...
Re: [gmx-users] Help! A dummy atom definition problem!
Wang Qin wrote: Hi Maik, I really did mix up a dummy atom with a virtual site. Any difference? Thank you very much for your help. we changed the name from dummy to virtual site a few years back. We didn't want to be associated with MD for dummies. Regards, Qin On 9/12/07, *Maik Goette* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: The problem actually is, that you mixed up a dummy atom with a virtual site, I guess. Virtual sites are not allowed to have a mass, as the error message claims. Also, a proper hydrogen should have a mass. If you want a hydrogen to appear, you have to place a particle in A-state which has no non-bonded interaction, i.e. LJ QQ interactions should be zero. If you want to prevent it from flying away, you should put bonded terms to the particle. In the B-state, the QQ and LJ should be there (whereas the LJ interaction for a hydrogen is 0 anyway). 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 opls_999 DUM 0 1.008000 0.000A 0.00 0.00 So, I expect, this is, how it should look like. Be aware of the missing bonded terms in the force field for a DUM particle. Maybe, you want to call it H instead... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de http://bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top, line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000 V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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] mailto:[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
[gmx-users] Distance Restraints Violations
Hi, all: Im using g_disre in gmx3.3.1 to calculate violations of distance restraints in a simulation and I saw the message: Fatal error: tpr inconsistency. ndr = 0, label = 1 The gmxdump of tpr shows functype[459]=DISRES, label= 1, type=1, low= 1.8007e-01, up1= 2.8001e-01, up2= 3.3013e-01, fac= 1.e+00) Im looking for hints in the gmx-users mail box and ... Usually problems here are related to the topology. Check whether one of the restraints is missing (typically the one with label = 362). This check is in g_disre only, not in mdrun or grompp. Maybe it should be in the latter... It seems that the restraint is there Am I forgeting something? Any hint will be sincerely appreciated! Im lost here! Francisco -- Francisco Gomes Neto Centro Nacional de Ressonancia Magnetica Nuclear - CNRMN Av. Brigadeiro Trompowisky, s/n - Predio CCS - Sala E-10 Rio de Janeiro - RJ - CEP 21.941-590 e-mail: [EMAIL PROTECTED] http://cnrmn.bioqmed.ufrj.br ___ 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
