Re: [gmx-users] frezzing a bond : NPT and NVT simulations
Nilesh Dhumal wrote: Then it looks there is bug ater define the constraints in itp file, bond distance changes. Then file a bugzilla so the developers can either confirm the bug and fix it, or provide an explanation as to what is going on. -Justin On Wed, August 4, 2010 10:22 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Its oscillate between +/- 3-4 A. If I freeze the distance by using freeze groups and dim in mdp file. It works perfectly for NVT simulations. It oscillate for NPT simulation. I don't know if there have been any changes (I don't see anything in the revision history), but as far as I know, freezing is incompatible with NPT ensembles due to the inability to scale the frozen coordinates. -Justin Nilesh On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: constraints = all-bonds is working. I have solvent molecule for which I don't want constraints on them. I can't use constraints = all-bonds for simulation. So you used g_dist to determine the distances with the setup shown below, but did you correct for PBC effects? Is there a systematic increase in the distance between the two particles, or does it oscillate? -Justin Nilesh On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello I am trying to constraints of a bond. I checked the distance using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it changes. Here I have pasted mdp file and itp file. Maybe there's a bug in the interpretation of the constraints? The combination of "constraints = none" + [constraints] directive should constrain the bond. Have you tried simply defining a [bonds] directive and using "constraints = all-bonds"? -Justin Nilesh Solvent.itp ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_997 PA 0 100.1.000 A 0.4e-01 0.82890e-01 opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 [ bondtypes ] ; ij func b0 kb PANE 10.35 00 [ moleculetype ] ; name nrexcl ABC 3 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 opls_9971 ABCPA 11. 100. 2 opls_9981 ABCNE 1 -1. 100.000 [ constraints ] 1 2 10.35000 pr.mdp title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001 ; ps ! nsteps = 25 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME vdwtype = cut-off rcoulomb= 1.0 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 400 ; Pressure coupling is not on Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 400.0 gen_seed = 173529 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 th
Re: [gmx-users] frezzing a bond : NPT and NVT simulations
Then it looks there is bug ater define the constraints in itp file, bond distance changes. On Wed, August 4, 2010 10:22 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Its oscillate between +/- 3-4 A. >> If I freeze the distance by using freeze groups and dim in mdp file. It >> works perfectly for NVT simulations. It oscillate for NPT simulation. > > I don't know if there have been any changes (I don't see anything in the > revision history), but as far as I know, freezing is incompatible with NPT > ensembles due to the inability to scale the frozen coordinates. > > -Justin > > >> Nilesh >> >> >> On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> constraints = all-bonds is working. I have solvent molecule for which I don't want constraints on them. I can't use constraints = all-bonds for simulation. >>> So you used g_dist to determine the distances with the setup shown >>> below, but did you correct for PBC effects? Is there a systematic >>> increase in the distance between the two particles, or does it >>> oscillate? >>> >>> -Justin >>> >>> >>> Nilesh On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote: > Nilesh Dhumal wrote: > > > >> Hello >> I am trying to constraints of a bond. I checked the distance >> using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone >> tell why it changes. Here I have pasted mdp file and itp file. >> > Maybe there's a bug in the interpretation of the constraints? > The > combination of "constraints = none" + [constraints] directive > should constrain the bond. Have you tried simply defining a > [bonds] > directive and using "constraints = all-bonds"? > > -Justin > > > > >> Nilesh >> Solvent.itp >> ; Derived from parsing of runfiles/alat.top.orig >> [ defaults ] >> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ >> ;1 3 yes 0.5 0.5 >> ; comb-rule 3 is square-root sigma, the OPLSAA version >> >> >> >> >> [ atomtypes ] >> ; full atom descriptions are available in ffoplsaa.atp >> ; name bond_typemasscharge ptype sigma >> epsilon opls_997 PA 0 100.1.000 A >> 0.4e-01 >> 0.82890e-01 >> opls_998 NE 0 100. -1.000 A0.4e-01 >> 0.82890e-01 >> >> >> >> [ bondtypes ] >> ; ij func b0 kb >> PANE 10.35 00 >> >> >> >> >> [ moleculetype ] >> ; name nrexcl >> ABC 3 >> >> >> >> >> [ atoms ] >> ; nr typeresnr residu atomcgnrcharge mass >> 1 opls_9971 ABCPA 11. >> 100. >> 2 opls_9981 ABCNE 1 -1. >> 100.000 >> >> >> >> >> [ constraints ] >> 1 2 10.35000 >> >> >> >> >> >> pr.mdp title = cpeptid position restraining cpp >> = >> /usr/bin/cpp >> constraints = none integrator = md dt = >> 0.001 >> ; ps ! >> nsteps = 25 ; total 1.0 ps. nstcomm = >> 1 >> nstxout = 10 nstvout = 1000 nstfout = >> 0 >> nstlog = 10 nstenergy = 10 nstlist = >> 10 >> ns_type = grid rlist = 1.0 >> coulombtype = PME >> vdwtype = cut-off rcoulomb= 1.0 rvdw = >> 1.4 >> fourierspacing = 0.12 fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 pme_order = 4 ewald_rtol = >> 1e-5 >> optimize_fft= yes constraint-algorithm = SHAKE ; >> Berendsen >> temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 >> tc-grps =system ref_t = 400 ; Pressure coupling is not on >> Pcoupl = no >> pcoupltype = isotropic tau_p = 0.5 >> compressibility = 4.5e-5 ref_p = 1.0 ; Generate >> velocites is on at 300 K. gen_vel = yes gen_temp >> = 400.0 gen_seed = >> 173529 >> >> >> >> >> > -- > > > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archi
Re: [gmx-users] frezzing a bond : NPT and NVT simulations
Nilesh Dhumal wrote: Its oscillate between +/- 3-4 A. If I freeze the distance by using freeze groups and dim in mdp file. It works perfectly for NVT simulations. It oscillate for NPT simulation. I don't know if there have been any changes (I don't see anything in the revision history), but as far as I know, freezing is incompatible with NPT ensembles due to the inability to scale the frozen coordinates. -Justin Nilesh On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: constraints = all-bonds is working. I have solvent molecule for which I don't want constraints on them. I can't use constraints = all-bonds for simulation. So you used g_dist to determine the distances with the setup shown below, but did you correct for PBC effects? Is there a systematic increase in the distance between the two particles, or does it oscillate? -Justin Nilesh On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello I am trying to constraints of a bond. I checked the distance using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it changes. Here I have pasted mdp file and itp file. Maybe there's a bug in the interpretation of the constraints? The combination of "constraints = none" + [constraints] directive should constrain the bond. Have you tried simply defining a [bonds] directive and using "constraints = all-bonds"? -Justin Nilesh Solvent.itp ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_997 PA 0 100.1.000 A0.4e-01 0.82890e-01 opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 [ bondtypes ] ; ij func b0 kb PANE 10.35 00 [ moleculetype ] ; name nrexcl ABC 3 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 opls_9971 ABCPA 11. 100. 2 opls_9981 ABCNE 1 -1. 100.000 [ constraints ] 1 2 10.35000 pr.mdp title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001 ; ps ! nsteps = 25 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME vdwtype = cut-off rcoulomb= 1.0 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 400 ; Pressure coupling is not on Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 400.0 gen_seed = 173529 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA j
Re: [gmx-users] frezzing a bond : NPT and NVT simulations
Its oscillate between +/- 3-4 A. If I freeze the distance by using freeze groups and dim in mdp file. It works perfectly for NVT simulations. It oscillate for NPT simulation. Nilesh On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> constraints = all-bonds is working. I have solvent molecule for which I >> don't want constraints on them. I can't use constraints = all-bonds >> for simulation. > > So you used g_dist to determine the distances with the setup shown below, > but did you correct for PBC effects? Is there a systematic increase in > the distance between the two particles, or does it oscillate? > > -Justin > > >> Nilesh >> >> >> On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> Hello I am trying to constraints of a bond. I checked the distance using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it changes. Here I have pasted mdp file and itp file. >>> Maybe there's a bug in the interpretation of the constraints? The >>> combination of "constraints = none" + [constraints] directive should >>> constrain the bond. Have you tried simply defining a [bonds] >>> directive and using "constraints = all-bonds"? >>> >>> -Justin >>> >>> >>> Nilesh Solvent.itp ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_997 PA 0 100.1.000 A0.4e-01 0.82890e-01 opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 [ bondtypes ] ; ij func b0 kb PANE 10.35 00 [ moleculetype ] ; name nrexcl ABC 3 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 opls_9971 ABCPA 11. 100. 2 opls_9981 ABCNE 1 -1. 100.000 [ constraints ] 1 2 10.35000 pr.mdp title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001 ; ps ! nsteps = 25 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME vdwtype = cut-off rcoulomb= 1.0 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 400 ; Pressure coupling is not on Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 400.0 gen_seed = 173529 >>> -- >>> >>> >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> >>> >>> -- >>> 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 >>> >>> >>> >>> >> >> >> > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > 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'
Re: [gmx-users] frezzing a bond : NPT and NVT simulations
Nilesh Dhumal wrote: constraints = all-bonds is working. I have solvent molecule for which I don't want constraints on them. I can't use constraints = all-bonds for simulation. So you used g_dist to determine the distances with the setup shown below, but did you correct for PBC effects? Is there a systematic increase in the distance between the two particles, or does it oscillate? -Justin Nilesh On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello I am trying to constraints of a bond. I checked the distance using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it changes. Here I have pasted mdp file and itp file. Maybe there's a bug in the interpretation of the constraints? The combination of "constraints = none" + [constraints] directive should constrain the bond. Have you tried simply defining a [bonds] directive and using "constraints = all-bonds"? -Justin Nilesh Solvent.itp ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_997 PA 0 100.1.000 A0.4e-01 0.82890e-01 opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 [ bondtypes ] ; ij func b0 kb PANE 10.35 00 [ moleculetype ] ; name nrexcl ABC 3 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 opls_9971 ABCPA 11. 100. 2 opls_9981 ABCNE 1 -1. 100.000 [ constraints ] 1 2 10.35000 pr.mdp title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001; ps ! nsteps = 25 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME vdwtype = cut-off rcoulomb= 1.0 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 400 ; Pressure coupling is not on Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 400.0 gen_seed = 173529 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] frezzing a bond : NPT and NVT simulations
constraints = all-bonds is working. I have solvent molecule for which I don't want constraints on them. I can't use constraints = all-bonds for simulation. Nilesh On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello >> I am trying to constraints of a bond. I checked the distance using >> g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it >> changes. Here I have pasted mdp file and itp file. >> > > Maybe there's a bug in the interpretation of the constraints? The > combination of "constraints = none" + [constraints] directive should > constrain the bond. Have you tried simply defining a [bonds] directive and > using "constraints = all-bonds"? > > -Justin > > >> Nilesh >> Solvent.itp >> ; Derived from parsing of runfiles/alat.top.orig >> [ defaults ] >> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ >> ;1 3 yes 0.5 0.5 >> ; comb-rule 3 is square-root sigma, the OPLSAA version >> >> >> [ atomtypes ] >> ; full atom descriptions are available in ffoplsaa.atp >> ; name bond_typemasscharge ptype sigma epsilon >> opls_997 PA 0 100.1.000 A0.4e-01 >> 0.82890e-01 >> opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 >> >> [ bondtypes ] >> ; ij func b0 kb >> PANE 10.35 00 >> >> >> [ moleculetype ] >> ; name nrexcl >> ABC 3 >> >> >> [ atoms ] >> ; nr typeresnr residu atomcgnrcharge mass >> 1 opls_9971 ABCPA 11. 100. >> 2 opls_9981 ABCNE 1 -1. 100.000 >> >> >> [ constraints ] >> 1 2 10.35000 >> >> >> >> pr.mdp title = cpeptid position restraining cpp >> = /usr/bin/cpp >> constraints = none integrator = md dt >> = 0.001; ps ! >> nsteps = 25 ; total 1.0 ps. nstcomm = >> 1 >> nstxout = 10 nstvout = 1000 nstfout >> = 0 >> nstlog = 10 nstenergy = 10 nstlist = >> 10 >> ns_type = grid rlist = 1.0 coulombtype >> = PME >> vdwtype = cut-off rcoulomb= 1.0 rvdw >> = 1.4 >> fourierspacing = 0.12 fourier_nx = 0 fourier_ny >> = 0 >> fourier_nz = 0 pme_order = 4 ewald_rtol = >> 1e-5 >> optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen >> temperature coupling is on Tcoupl = v-rescale >> tau_t = 0.1 tc-grps =system ref_t = 400 ; Pressure coupling is not on >> Pcoupl = no >> pcoupltype = isotropic tau_p = 0.5 compressibility >> = 4.5e-5 >> ref_p = 1.0 ; Generate velocites is on at 300 K. >> gen_vel = yes gen_temp= 400.0 gen_seed >> = 173529 >> >> >> > > -- > > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > 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 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] frezzing a bond : NPT and NVT simulations
Nilesh Dhumal wrote: Hello I am trying to constraints of a bond. I checked the distance using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it changes. Here I have pasted mdp file and itp file. Maybe there's a bug in the interpretation of the constraints? The combination of "constraints = none" + [constraints] directive should constrain the bond. Have you tried simply defining a [bonds] directive and using "constraints = all-bonds"? -Justin Nilesh Solvent.itp ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_997 PA 0 100.1.000 A0.4e-01 0.82890e-01 opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 [ bondtypes ] ; ij func b0 kb PANE 10.35 00 [ moleculetype ] ; name nrexcl ABC 3 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 opls_9971 ABCPA 11. 100. 2 opls_9981 ABCNE 1 -1. 100.000 [ constraints ] 1 2 10.35000 pr.mdp title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001; ps ! nsteps = 25 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME vdwtype = cut-off rcoulomb= 1.0 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 400 ; Pressure coupling is not on Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 400.0 gen_seed= 173529 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] frezzing a bond : NPT and NVT simulations
Hello I am trying to constraints of a bond. I checked the distance using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it changes. Here I have pasted mdp file and itp file. Nilesh Solvent.itp ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_997 PA 0 100.1.000 A0.4e-01 0.82890e-01 opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 [ bondtypes ] ; ij func b0 kb PANE 10.35 00 [ moleculetype ] ; name nrexcl ABC 3 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 opls_9971 ABCPA 11. 100. 2 opls_9981 ABCNE 1 -1. 100.000 [ constraints ] 1 2 10.35000 pr.mdp title = cpeptid position restraining cpp = /usr/bin/cpp constraints = none integrator = md dt = 0.001; ps ! nsteps = 25 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME vdwtype = cut-off rcoulomb= 1.0 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes constraint-algorithm = SHAKE ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 400 ; Pressure coupling is not on Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 400.0 gen_seed= 173529 -- 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] frezzing a bond : NPT and NVT simulations
Hello, I am trying to freeze a bond (3.5 A) in my system. I used the index file to define group and I added this two lines in my .mdp file. freezegrps = PA NE freezedim = Y Y Y Y Y Y I used g_dist to verify the distance between the freezing atoms. During the NVT simulation the distace is around 3.449 A and its constant though out the simulation. For NPT simulation the distance varies from 3.449 to 3.1. Can you tell why distance changes in NPT not in NVT. How can I freeze a bond om NPT simulation? Nilesh -- 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] frezzing a bond
Justin A. Lemkul wrote: > Nilesh Dhumal wrote: >> How can I freeze a bond? > How about distance restraints instead? That raises some kind of off-topic question: In Cerius2, we use position constraints to reduce the calculation complexity, because forces between constrained atoms need not to be evaluated, this saves some simulation time. And, in our group, that's practically the only reason to do so. Now, if I recall corectly, postion and distance restraints are like stiff springs keeping the atom in a certain distance/position. Does this take more, less or the same computation time as if the bonds were free? Is it possible to use constraints in gromacs as I mentioned above? Thanks -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- 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] frezzing a bond
Nilesh Dhumal wrote: Hello, I am trying to freeze a bond (3.5 A) in my system. I used the index file to define group and I added this two lines in my .mdp file. freezegrps = PA NE freezedim = Y Y Y Y Y Y I used g_dist to verify the distance between the freezing atoms and it turned out 3.9 A. I checked my .itp also (distance is 3.5). How can I freeze a bond? How about distance restraints instead? Seems like an applicable situation. Or, just define the actual bond in your topology and use constraints. -Justin Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] frezzing a bond
Hello, I am trying to freeze a bond (3.5 A) in my system. I used the index file to define group and I added this two lines in my .mdp file. freezegrps = PA NE freezedim = Y Y Y Y Y Y I used g_dist to verify the distance between the freezing atoms and it turned out 3.9 A. I checked my .itp also (distance is 3.5). How can I freeze a bond? Nilesh -- 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
