[gmx-users] need help with topology file
Hi, I am trying to use two types of force fields for my system which has protein and fullerene. i want to use OPLS for protein and ffG53a6 for fullerene(as i don't have opls readily available for this). When i use two itp files in #include section grompp does not allow me to do that with the following error. --- Program grompp, VERSION 4.0.5 Source code file: topio.c, line: 430 Fatal error: Syntax error - File ffG53a6.itp, line 6 Last line read: ' 1 1 no 1.0 1.0' Found a second defaults directive. --- Chapter 5 in manual has information about using topology files but i am not clear about using #define. Can anybody help me how to use opls for protein and gromos for fullerene in the same system? Thanks in advance. Srinivas. -- * *J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics, Drexel University 3141 Chestnut St, Philadelphia, PA 19104 Ph: 215-895-1989 Web:http://jsrao.web.officelive.com/default.aspx* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] problem with fullerene simulations
Hi Gromacs users, I am trying to run a fullerene simulaton in TIP4P water model, i am using the c70_G53a6.itp http://tfy.tkk.fi/soft/downloads/files/c70_G53a6.itp file downloaded from http://tfy.tkk.fi/soft/downloads/. i have added TIP4P water model using genbox command, later when i am trying to generate .tpr file for energy minimization it gives me the following error. --- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OWT4 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I looked up in the mailing list and found many helpful comments but i could not resolve the problem, i searched in the tip4p.itp file of gromos force field and i could see that tip4p water model is defined in that file, but i could not find the atom types defined in atomtypes.atp file. when i try to enter the atom types for some reason it does not read my entries. here is my .top file ; The force field files to be included #include ffG53a6.itp [ moleculetype ] #include fullerene.itp ; Include water topology #include tip4p.itp [ system ] Fullerene in Water [ molecule ] FUL 1 SOL 1696 Can anybody help me? Thanks very much. -- * *J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics, Drexel University 3141 Chestnut St, Philadelphia, PA 19104 Ph: 215-895-1989 Web:http://jsrao.web.officelive.com/default.aspx* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem with fullerene simulations
Hi Justin, Thanks for your reply, i have no particular choice i was using it for my other work and just started with it. Now i tried it again with spc model, I still get the following error. ++ Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OWT3 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ++ I could see these atoms are defined in .itp file of gromos force filed, but i suspect some thing is going wrong with atom types in .atp file. any suggestions? Thanks Srinivs. On Fri, Jul 22, 2011 at 5:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: jampani srinivas wrote: Hi Gromacs users, I am trying to run a fullerene simulaton in TIP4P water model, i am using the c70_G53a6.itp http://tfy.tkk.fi/soft/** downloads/files/c70_G53a6.itphttp://tfy.tkk.fi/soft/downloads/files/c70_G53a6.itp ** file downloaded from http://tfy.tkk.fi/soft/**downloads/http://tfy.tkk.fi/soft/downloads/. i have added TIP4P water model using genbox command, later when i am trying to generate .tpr file for energy minimization it gives me the following error. --**- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OWT4 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- I looked up in the mailing list and found many helpful comments but i could not resolve the problem, i searched in the tip4p.itp file of gromos force field and i could see that tip4p water model is defined in that file, but i could not find the atom types defined in atomtypes.atp file. when i try to enter the atom types for some reason it does not read my entries. This may or may not be related to a bug that has been fixed in the development version of the code. Simply adding OWT4 into atomtypes.atp is insufficient; you need to add nonbonded parameters in ffnonbonded.itp as well. Without seeing the actual error message(s) you're getting, I don't dare guess further. here is my .top file ; The force field files to be included #include ffG53a6.itp [ moleculetype ] #include fullerene.itp ; Include water topology #include tip4p.itp [ system ] Fullerene in Water [ molecule ] FUL 1 SOL 1696 Can anybody help me? Is there a particular reason you need to use TIP4P? The Gromos force fields were parameterized with SPC water, so that's what is expected to work. In principle, you should be able to use any water model you want, but you still have to demonstrate that it's a valid approach. -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- * *J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics, Drexel University 3141 Chestnut St, Philadelphia, PA 19104 Ph: 215-895-1989 Web:http://jsrao.web.officelive.com/default.aspx* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] problem with fullerene simulations
Oh sorry, i used spc.itp now and it works. Thanks. Srinivas. On Fri, Jul 22, 2011 at 5:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: jampani srinivas wrote: Hi Justin, Thanks for your reply, i have no particular choice i was using it for my other work and just started with it. Now i tried it again with spc model, I still get the following error. ++** Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OWT3 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors ++** The error indicates you're trying to use TIP3P, not SPC. I could see these atoms are defined in .itp file of gromos force filed, but i suspect some thing is going wrong with atom types in .atp file. any suggestions? Use SPC or SPC/E, they're the only models that actually seem to work with Gromos96. -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- * *J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics, Drexel University 3141 Chestnut St, Philadelphia, PA 19104 Ph: 215-895-1989 Web:http://jsrao.web.officelive.com/default.aspx* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] domain decomposition
Hi Try with -dd 2 x 2 x 2 option with 8 nodes and check the performance. I too got the same problems, i could overcome with symmetrical -dd option. Srinivas. On Fri, May 7, 2010 at 8:57 AM, irene farabella i.farabe...@mail.cryst.bbk.ac.uk wrote: Hello! I am new to Gromacs and especially at parallel runs. I have some problem running my system using domain decomposition. I apologize but it will be a long mail... My system is made up by a membrane protein embedded is a mixed lipid bilayer (POPE/POPG). I tried to run it on 8 nodes but the simulation crashed due to A charge group moved too far between two domain decomposition steps and high % of load imbalance between nodes. I then tested the same run on a single node and it worked. I tried then different amount of nodes, changing DD (using mdrun -dd option) and it seems that more node I am using the less the performance in terms of ns/day although the load imbalance % is highly variable. During this test I found that the optimal nodes for my system is running it on 6 node with a DD 3:2:1 (vol 0.80 imb F 1% ) from the log file: Initializing Domain Decomposition on 6 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.703 nm, LJ-14, atoms 21579 21587 multi-body bonded interactions: 2.038 nm, Proper Dih., atoms 20434 20405 Minimum cell size due to bonded interactions: 2.241 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.820 nm Estimated maximum distance required for P-LINCS: 0.820 nm Domain decomposition grid 3 x 2 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. ... Making 2D domain decomposition grid 3 x 2 x 1, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: Protein_POPE_POPG 1: SOL_NA+_CL- There are: 82711 Atoms Charge group distribution at step 200: 5512 5533 5668 5694 5535 5626 Grid: 7 x 10 x 14 cells Initial temperature: 309.243 K Using this setting I finally managed to equilibrate my system by going trough a series of restrained runs. Surprisingly after 6,5 ns of non-restrained run (Step 3289500) the simulation crashes with : Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated . It seems strange that it crashes only at 3289500 steps of a non-restrained run. I am now running a short run starting from a short while before the crash step using a single processor and, as suspected, it is going smoothly. My guess is that something is going wrong with the domain decomposition of a such non-homogeneous system, considering that there are also charged lipids that complicate it but I have no idea how to solve/improve it. I am using gromacs-4.0.5. Any suggestion are welcome. -- Irene Farabella Wellcome Trust PhD student Institute of Structural and Molecular Biology Department of of Biological Sciences Birkbeck University of London Malet Street London WC1E 7HX Telephone +44 (0)20 7631 6815 -- 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 -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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] RE: [Bug 404] energy increase in nvt and nve simiulations
Dear Berk, Yes the system is stable and the small velocity appears only at step 0 as you said. This looks fine now, Thanks a lot for you continuous support Thanks very much. Srinivas. On Mon, Apr 26, 2010 at 7:43 AM, Berk Hess g...@hotmail.com wrote: Hi, So the system seems to be stable now? The water molecules might get a very small velocity, because constraints are always applied. If your starting coordinates do not have full precision (e.g. gro or pdb), a minor correction and thus velocity will occur at step 0 only. This should not be an issue. Berk -- Date: Sun, 25 Apr 2010 11:59:36 -0400 Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, First of all thanks very much for your kind patience and help. As a new user i am facing some problems and not clear about many options and how to use them. I was reading several messages of yours from mailing list which are very close to my problem. After reading several of them from mailing list i have carefully tuned my md.mdp file and the energy out put from g_energy is here. +++ Last energy frame read 1000 time 2000.000 Statistics over 101 steps [ 0. thru 2000.0001 ps ], 1 data sets All averages are exact over 101 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Total Energy -55074.6348.391347.979 -0.0293271 -58.6543 +++ Energy looks pretty stable compare to the one i have reported in Bugzilla, in which i always use to get the drift from 200 to 600, and finally it ends up with positive energy. Here is the md.mdp file i have used for my current simulation. title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 100.0 ns. nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 comm_mode = none nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 283.00.0 ;Generate velocites is on at 300 K. gen_vel = yes gen_temp= 283.0 energygrps = Tmp1 Tmp2 energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1 gen_seed= 181726 freezegrps = Tmp2 freezedim = Y Y Y +++ I still have small question here, when i try to print the velocities from trajectory i found that some of the frozen water too get the velocities (i have complied my gromcas with md.c Fixed velocity output at first step on nodes1 with PD and frozen groups). Here is the example for few frozen water. ++ 48SOL OW 149 1.630 1.491 6.061-0.0001 -0. -0. 48SOLHW1 150 1.555 1.541 6.027-0.0001 0.0001 -0. . . . 9503SOL OW31669 6.075 6.430 0.0970.0001 0. -0. 9503SOLHW131670 5.984 6.437 0.1260. 0.0001 -0. 9503SOLHW231671 6.089 6.508 0.044 -0.0001 0.0001 -0. ++ I am not very clear why i am still getting this velocity, and how would these velocities to frozen atoms effect the simulation? Can you please give me your suggestions. Thanks in advance Srinivas. -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 ** -- New Windows 7: Find the right PC for you. Learn more.http://windows.microsoft.com/shop -- 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
Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations
Dear Berk, First of all thanks very much for your kind patience and help. As a new user i am facing some problems and not clear about many options and how to use them. I was reading several messages of yours from mailing list which are very close to my problem. After reading several of them from mailing list i have carefully tuned my md.mdp file and the energy out put from g_energy is here. +++ Last energy frame read 1000 time 2000.000 Statistics over 101 steps [ 0. thru 2000.0001 ps ], 1 data sets All averages are exact over 101 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Total Energy -55074.6348.391347.979 -0.0293271 -58.6543 +++ Energy looks pretty stable compare to the one i have reported in Bugzilla, in which i always use to get the drift from 200 to 600, and finally it ends up with positive energy. Here is the md.mdp file i have used for my current simulation. title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 100.0 ns. nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 comm_mode = none nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 283.00.0 ;Generate velocites is on at 300 K. gen_vel = yes gen_temp= 283.0 energygrps = Tmp1 Tmp2 energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1 gen_seed= 181726 freezegrps = Tmp2 freezedim = Y Y Y +++ I still have small question here, when i try to print the velocities from trajectory i found that some of the frozen water too get the velocities (i have complied my gromcas with md.c Fixed velocity output at first step on nodes1 with PD and frozen groups). Here is the example for few frozen water. ++ 48SOL OW 149 1.630 1.491 6.061-0.0001 -0. -0. 48SOLHW1 150 1.555 1.541 6.027-0.0001 0.0001 -0. . . . 9503SOL OW31669 6.075 6.430 0.0970.0001 0. -0. 9503SOLHW131670 5.984 6.437 0.1260. 0.0001 -0. 9503SOLHW231671 6.089 6.508 0.044 -0.0001 0.0001 -0. ++ I am not very clear why i am still getting this velocity, and how would these velocities to frozen atoms effect the simulation? Can you please give me your suggestions. Thanks in advance Srinivas. -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 ** -- 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] RE: [Bug 404] energy increase in nvt and nve simiulations
Dear Berk, I have run it for 5ns, as you said for first 1ns i have not seen much drift in the energy there after energy is slowly increasing in each step. Should i run it again and send you the edr file? can you please let me know on which version of gromacs you have run this file? Thanks very much Srinivas. On Thu, Apr 22, 2010 at 3:25 AM, Berk Hess g...@hotmail.com wrote: Hi, I quickly ran the tpr file you provided on bugzilla, but I don't see an enormous energy drift. What do you mean with the energy explodes? Berk -- Date: Wed, 21 Apr 2010 11:18:53 -0400 Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, I am sorry for poor communication, Herewith i am giving my md.mdp file. I this file as you could see i am using two temp coupling groups Tmp1 is protein and a 2nm spherical layer of water around it, and the second one Tmp2 which has only water. Now i want to fix the Tmp2 and apply 0 K to it. As you could see that from the file below i have taken Tcoupl = V-rescale and two coupling groups Tmp1 and Tmp2 to make a frozen wall. I am not accelerating any group here. In other words the goal of simulation is to check the behavior of protein is a confined sphere, i am trying to make frozen wall by freezing water around the protein after a specified distance. title = SS2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 0 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 283.00.0 gen_vel = yes gen_temp= 283.0 gen_seed= 181726 freezegrps = Tmp2 freezedim = Y Y Y Thanks very much Srinivas. On Wed, Apr 21, 2010 at 10:53 AM, Berk Hess g...@hotmail.com wrote: Hi, I moved this to the user list, so it will be of use to others. I have no clue what you are trying to do, what groups you are accelerating or freezing. So we can't help you without further information. Setting up simulations with frozen groups, accelerate groups or different coupling temperatures is tricky and will in most cases destroy energy conservation. Berk -- Date: Wed, 21 Apr 2010 10:41:25 -0400 Subject: Fwd: [Bug 404] energy increase in nvt and nve simiulations From: jampa...@gmail.com To: g...@hotmail.com Dear Berk, Thanks for the reply, based on the suggestions of Justin from Mailing list i have tried the simulation in the following way. 1. I have removed the acc_grps option 2. I have used energygrp_excl to avoid interaction between non frozen-frozen and frozen-frozen. Still i have seen some velocity to the frozen atoms (i have printed velocities from trajectory) and drift in the energy. 3. I also switched of PBC and used coulombtype = different options here In this case i observed that some of the water molecules try to escape from the system. But i am not clear about center of mass motion. Should i allow to change center of mass with comm_mode = No option? Could you please let me know if you want more details about this? I am still struggling with running this simulation. Thanks for your kind help Srinivas. -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- New Windows 7: Find the right PC for you. Learn more.http://windows.microsoft.com/shop -- 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 -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University
Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations
Dear Berk, I am sorry for poor communication, Herewith i am giving my md.mdp file. I this file as you could see i am using two temp coupling groups Tmp1 is protein and a 2nm spherical layer of water around it, and the second one Tmp2 which has only water. Now i want to fix the Tmp2 and apply 0 K to it. As you could see that from the file below i have taken Tcoupl = V-rescale and two coupling groups Tmp1 and Tmp2 to make a frozen wall. I am not accelerating any group here. In other words the goal of simulation is to check the behavior of protein is a confined sphere, i am trying to make frozen wall by freezing water around the protein after a specified distance. title = SS2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 0 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 283.00.0 gen_vel = yes gen_temp= 283.0 gen_seed= 181726 freezegrps = Tmp2 freezedim = Y Y Y Thanks very much Srinivas. On Wed, Apr 21, 2010 at 10:53 AM, Berk Hess g...@hotmail.com wrote: Hi, I moved this to the user list, so it will be of use to others. I have no clue what you are trying to do, what groups you are accelerating or freezing. So we can't help you without further information. Setting up simulations with frozen groups, accelerate groups or different coupling temperatures is tricky and will in most cases destroy energy conservation. Berk -- Date: Wed, 21 Apr 2010 10:41:25 -0400 Subject: Fwd: [Bug 404] energy increase in nvt and nve simiulations From: jampa...@gmail.com To: g...@hotmail.com Dear Berk, Thanks for the reply, based on the suggestions of Justin from Mailing list i have tried the simulation in the following way. 1. I have removed the acc_grps option 2. I have used energygrp_excl to avoid interaction between non frozen-frozen and frozen-frozen. Still i have seen some velocity to the frozen atoms (i have printed velocities from trajectory) and drift in the energy. 3. I also switched of PBC and used coulombtype = different options here In this case i observed that some of the water molecules try to escape from the system. But i am not clear about center of mass motion. Should i allow to change center of mass with comm_mode = No option? Could you please let me know if you want more details about this? I am still struggling with running this simulation. Thanks for your kind help Srinivas. -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- New Windows 7: Find the right PC for you. Learn more.http://windows.microsoft.com/shop -- 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 -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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] problem with total energy
Dear Mark and Justin, Thanks for your help, as a beginner to GROMACS i think i have to spend even more time with each option and make sure i know what i am doing. I will spend some time by using different electrostatic options with out pbc and let you know what happens to the simulations. Thanks Srinivas. On Fri, Apr 9, 2010 at 1:26 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/04/2010 1:25 PM, jampani srinivas wrote: Dear Justin, I am sorry for the poor description of the problem, OK let me explain you clearly here. I have taken a decapeptide and solvated it with box size 6.0 nm, I want to create a frozen wall (confined sphere) around protein after a certain radius (in this case it is 2.5 nm). To achieve this i made two temperature coupling groups, first (Tmp1) one has protein and waters within 2.5nm from the center of the box and rest is second temperature coupling group (Tmp2). Initially when i run the simulation it was creating nrdf = 0 for both groups, Berk has helped me with a file readir.c file, i compiled my gromacs again that problem was solved. I have submitted simulations again and found that the energy was blowing up. I think you know the story after this. Earlier I want protein to interact with inner wall of the frozen group and check what happens, because of this I have never looked at the energygrps_excl option. I have done with both 2 and 4 fs time steps and I took 4fs option to speed up the simulation, and I have to still look at the paper you suggested me. Thanks for your suggestions, I have implemented your suggestion one after the other, finally when i use the energygrps_excl option it worked out. Now there is no sudden drift in the energy, and also i checked the velocities of non-frozen group is mostly zero (except for first frame) When I use the energygrps_excel option in the following way i am getting the below mentioned note i have to still understand what is this message. On the other hand if i use only energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1 line in mdp file i am getting fatal error. Is it necessary to to define the energy groups first and later exclude the energy option? Yes, energy group exclusions require matching energy group definitions. The relevant part of manual 7.3 probably says this. + energygrps = Tmp1 Tmp2 energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1 NOTE Can not exclude the lattice Coulomb energy between energy groups You seem to be trying to simulate a droplet inside a rigid shell of water. If so, why do you want the system to be periodic? You don't want periodicity artefacts *and* frozen-water-shell artefacts. There are other electrostatics models better suited than PME to such situations. You should look in the literature for successful published methodologies, rather than risk inventing a square wheel yourself before you've got enough experience to be confident with what you're doing. Here, the reciprocal-space part of the PME calculation must contain contributions from your excluded energy-groups, so you've got some Frankenstein possible worst-of-all-worlds combination. If I got such a paper to review, I'd need to see some serious groundwork justifying such a choice. I used -maxwarn option here and generated the tpr file. I hope this does not harm the simulation. That's a risky strategy. The programmer didn't put in such a message just to see whether he could do it... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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] problem with total energy
Hi Thanks for your response, I am allowing the two groups (frozen and non-frozen) groups interact each other, i guess i am getting the energy of total system from g_energy. I checked the velocities of frozen group atoms, they are not zero. I have seen in git master that this problem was fixed and updated in md.c file, I have downloaded this from git master and compiled my gromacs again still i found that frozen atoms gets the initial velocity. I am not at all clear why the energy of system should blow up, can you please help me if there is solution for this. Thanks in advance. Srinivas. On Wed, Apr 7, 2010 at 4:47 PM, ms deviceran...@gmail.com wrote: jampani srinivas ha scritto: Dear Berk, I am sorry if i am confusing you with my poor description of problem, actually I have submitted simulation with two temperature coupling groups (i think you already know that from our earlier conversations) and found that there is a continuous increase in the total energy of the system. I could not observe any blowing in the output file but the system energy is continuously increasing, i am using 4fs time step here. Can you please let me know if i have to give more details? Which part of the system is increasing its energy? m. -- 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 -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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] problem with total energy
Dear Justin, Thanks for your responce. Here is my mdp file. +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.004 ; ps ! nsteps = 2500 ; total 100.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 283.00.0 gen_vel = yes gen_temp= 283.0 acc_grps= Tmp1 accelerate = 0.1 0.1 0.1 gen_seed= 181726 freezegrps = Tmp2 freezedim = Y Y Y Thanks Srinivas. On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: jampani srinivas wrote: Hi Thanks for your response, I am allowing the two groups (frozen and non-frozen) groups interact each other, i guess i am getting the energy of total system from g_energy. I checked the velocities of frozen group atoms, they are not zero. I have seen in git master that this problem was fixed and updated in md.c file, I have downloaded this from git master and compiled my gromacs again still i found that frozen atoms gets the initial velocity. I am not at all clear why the energy of system should blow up, can you please help me if there is solution for this. I haven't been following this closely; can you post an .mdp file? -Justin Thanks in advance. Srinivas. On Wed, Apr 7, 2010 at 4:47 PM, ms deviceran...@gmail.com mailto: deviceran...@gmail.com wrote: jampani srinivas ha scritto: Dear Berk, I am sorry if i am confusing you with my poor description of problem, actually I have submitted simulation with two temperature coupling groups (i think you already know that from our earlier conversations) and found that there is a continuous increase in the total energy of the system. I could not observe any blowing in the output file but the system energy is continuously increasing, i am using 4fs time step here. Can you please let me know if i have to give more details? Which part of the system is increasing its energy? m. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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 -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, Sorry to come up with some problems. As I mentioned to earlier, the simulations were running fine by generating non-zero ndrf value for non-frozen and zero nrdf value for frozen atoms. Unfortunately i could see that there is a continuous increase in the energy of the system. Do i need to change any parameter in my md.mdp file or something else? I run a short minimization before submitting production run, energy is converged after 4000 steps and i have taken the same system and applied freezing options and run the production run. Is there anything wrong in my procedure? can you please help me to solve this problem? Thanks very much for your kind help. Srinivas. On Wed, Mar 17, 2010 at 8:25 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, Sorry for the delayed reply, We have compiled the gromacs with readir.c that you have sent me, now it is working fine. Thank you very much for your kind help. Srinivas. On Wed, Mar 3, 2010 at 1:56 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, Thanks for your reply, I have just submitted all my files to bugzilla.gromacs.org. I got the bug # 400. Thanks very much Srinivas. On Wed, Mar 3, 2010 at 4:15 AM, Berk Hess g...@hotmail.com wrote: Hi, I don't know exactly what you have done, so currently I can say more than I have done already. Could you please file a bugzilla at bugzilla.gromacs.org and attach all the files required to run grompp? Thanks, Berk -- Date: Tue, 2 Mar 2010 21:11:06 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your previous responses, Can you please let me know if you have any solution for the size of freezing groups? I am still not able to do if i have larger freezing groups. Thanks again for your kind help. srinivas. On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I have checked my inputs and tcl scripts that i have used for the selection, i could see that my selection doesn't have any problem. I submitted it again still i am getting the same log file with nrdf 0 for non-freezing group. Please let me know if you want see any of my input files, and help me if you have solution for this problem. Thanks and Regards Srinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help. Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk -- Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com
[gmx-users] continuous energy increase in NVT and NVE simulations
Dear All, I am running MD simulation with TIP4P water and OPLS force field in NVT and NVE. I have noticed a continuous energy increase in both NVE and NVT simulations when i freeze a selected portion of my system. Recently i had problem with temperature coupling, Berk has sent me a file which has solved the problem of generating zero nrdf value. Now when i run the simulation with two temperature coupling groups(one is for frozen and second one is for non frozen) i have noticed the energy is continuously increasing. Even if i don't use the temperature coupling similar observation was made. Can anybody help me why it is happening? Thanks in advance Srinivas. -- * J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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] T-coupling groups
Dear Zuzana, Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from both groups. Srinivs. On Thu, Mar 18, 2010 at 4:55 PM, Zuzana Benkova zuzana.benk...@savba.skwrote: Dear GROMACS users, I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant section is as follows Tcoupl = nose-hoover tc-grps = PEO SOL tau_t = 0.1 0.1 ref_t = 50 50 gen_vel = yes gen_temp= 50 50 I have generated an index file where I have defined the PEO group. The [ SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. This matches with the gro file. I tried to prepare a tpr file using grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p topol.top -o PEO18_2900TIP3P_50K and got message Program grompp, VERSION 4.0.3 Source code file: readir.c, line: 1050 Fatal error: 16 atoms are not part of any of the T-Coupling groups I tried the compilations with 4.0.3 and 4.0.5 versions but the message was the same. I would be really thankful for an advice which can move me further. Thank you in advance. Zuzana -- 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 -- * J. Srinivasa Rao Ph.D. Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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] problem with the size of freeze groups
Dear Berk, Sorry for the delayed reply, We have compiled the gromacs with readir.c that you have sent me, now it is working fine. Thank you very much for your kind help. Srinivas. On Wed, Mar 3, 2010 at 1:56 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, Thanks for your reply, I have just submitted all my files to bugzilla.gromacs.org. I got the bug # 400. Thanks very much Srinivas. On Wed, Mar 3, 2010 at 4:15 AM, Berk Hess g...@hotmail.com wrote: Hi, I don't know exactly what you have done, so currently I can say more than I have done already. Could you please file a bugzilla at bugzilla.gromacs.org and attach all the files required to run grompp? Thanks, Berk -- Date: Tue, 2 Mar 2010 21:11:06 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your previous responses, Can you please let me know if you have any solution for the size of freezing groups? I am still not able to do if i have larger freezing groups. Thanks again for your kind help. srinivas. On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I have checked my inputs and tcl scripts that i have used for the selection, i could see that my selection doesn't have any problem. I submitted it again still i am getting the same log file with nrdf 0 for non-freezing group. Please let me know if you want see any of my input files, and help me if you have solution for this problem. Thanks and Regards Srinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help. Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk -- Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, Thanks for your reply, I have just submitted all my files to bugzilla.gromacs.org. I got the bug # 400. Thanks very much Srinivas. On Wed, Mar 3, 2010 at 4:15 AM, Berk Hess g...@hotmail.com wrote: Hi, I don't know exactly what you have done, so currently I can say more than I have done already. Could you please file a bugzilla at bugzilla.gromacs.org and attach all the files required to run grompp? Thanks, Berk -- Date: Tue, 2 Mar 2010 21:11:06 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your previous responses, Can you please let me know if you have any solution for the size of freezing groups? I am still not able to do if i have larger freezing groups. Thanks again for your kind help. srinivas. On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I have checked my inputs and tcl scripts that i have used for the selection, i could see that my selection doesn't have any problem. I submitted it again still i am getting the same log file with nrdf 0 for non-freezing group. Please let me know if you want see any of my input files, and help me if you have solution for this problem. Thanks and Regards Srinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help. Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk -- Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, Thanks for your previous responses, Can you please let me know if you have any solution for the size of freezing groups? I am still not able to do if i have larger freezing groups. Thanks again for your kind help. srinivas. On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I have checked my inputs and tcl scripts that i have used for the selection, i could see that my selection doesn't have any problem. I submitted it again still i am getting the same log file with nrdf 0 for non-freezing group. Please let me know if you want see any of my input files, and help me if you have solution for this problem. Thanks and Regards Srinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help. Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk -- Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Tmp2 freezedim = Y Y Y +++ On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess g...@hotmail.com wrote: Hi, It seems there is a bug in grompp, which subtracts degrees of freedom for constraints in water also for frozen water molecules. I guess the md.log file reports zero degrees of freedom for your t-coupl group. You can circumvent this issue by putting all your frozen atoms in a separate t-coupling group. Berk -- Date: Wed, 24 Feb 2010 21:34:30 -0500 From: jampa...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] problem with the size of freeze groups Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for MD, and temp coupling is applied for freezing and non freezing waters separately. In case of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 cm2/s (comparable with bulk), but the system with 25 Å radius gives me almost 0 diffusion coefficient. When I open the log file of 25 Å system it shows the initial temperature as zero. Is there any relation between size of freezing group and temperature coupling? How the sphere with 35 Å radius is working fine but not with the radius 25 Å? Can anybody help me? Here is my m.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Freez freezedim = Y Y Y +++ -- * J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104 Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- Express yourself instantly with MSN Messenger! MSN Messengerhttp://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- 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] problem with the size of freeze groups
HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Tmp2 freezedim = Y Y Y +++ On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess g...@hotmail.com wrote: Hi, It seems there is a bug in grompp, which subtracts degrees of freedom for constraints in water also for frozen water molecules. I guess the md.log file reports zero degrees of freedom for your t-coupl group. You can circumvent this issue by putting all your frozen atoms in a separate t-coupling group. Berk -- Date: Wed, 24 Feb 2010 21:34:30 -0500 From: jampa...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] problem with the size of freeze groups Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for MD, and temp coupling is applied for freezing and non freezing waters separately. In case of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 cm2/s (comparable with bulk), but the system with 25 Å radius gives me almost 0 diffusion coefficient. When I open the log file of 25 Å system it shows the initial temperature as zero. Is there any relation between size of freezing group and temperature coupling? How the sphere with 35 Å radius is working fine but not with the radius 25 Å? Can anybody help me? Here is my m.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Freez freezedim = Y Y Y +++ -- * J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104 Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx
Re: [gmx-users] problem with the size of freeze groups
Hi Berk, I am extremely sorry, here is the correct log file grpopts: nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Tmp2 freezedim = Y Y Y +++ On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess g...@hotmail.com wrote: Hi, It seems there is a bug in grompp, which subtracts degrees of freedom for constraints in water also for frozen water molecules. I guess the md.log file reports zero degrees of freedom for your t-coupl group. You can circumvent this issue by putting all your frozen atoms in a separate t-coupling group. Berk -- Date: Wed, 24 Feb 2010 21:34:30 -0500 From: jampa...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] problem with the size of freeze groups Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for MD, and temp coupling is applied for freezing and non freezing waters separately. In case of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 cm2/s (comparable with bulk), but the system with 25 Å radius gives me almost 0 diffusion coefficient. When I open the log file of 25 Å system it shows the initial temperature as zero. Is there any relation between size of freezing group and temperature coupling? How the sphere with 35 Å radius is working fine but not with the radius 25 Å? Can anybody help me? Here is my m.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Tmp2 freezedim = Y Y Y +++ On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess g...@hotmail.com wrote: Hi, It seems there is a bug in grompp, which subtracts degrees of freedom for constraints in water also for frozen water molecules. I guess the md.log file reports zero degrees of freedom for your t-coupl group. You can circumvent this issue by putting all your frozen atoms in a separate t-coupling group. Berk -- Date: Wed, 24 Feb 2010 21:34:30 -0500 From: jampa...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] problem with the size of freeze groups Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for MD, and temp coupling is applied for freezing and non freezing waters separately. In case of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 cm2/s (comparable with bulk), but the system with 25 Å radius gives me almost 0 diffusion coefficient. When I open the log file of 25 Å system it shows the initial temperature as zero. Is there any relation between size of freezing group and temperature coupling? How the sphere with 35 Å radius is working fine but not with the radius 25 Å? Can anybody help me? Here is my m.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Tmp2 freezedim = Y Y Y +++ On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess g...@hotmail.com wrote: Hi, It seems there is a bug in grompp, which subtracts degrees of freedom for constraints in water also for frozen water molecules. I guess the md.log file reports zero degrees of freedom for your t-coupl group. You can circumvent this issue by putting all your frozen atoms in a separate t-coupling group. Berk -- Date: Wed, 24 Feb 2010 21:34:30 -0500 From: jampa...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] problem with the size of freeze groups Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for MD, and temp coupling is applied for freezing and non freezing waters separately. In case of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 cm2/s (comparable with bulk), but the system with 25 Å radius gives me almost 0 diffusion coefficient. When I open the log file of
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help. Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk -- Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Tmp2 freezedim = Y Y Y +++ On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess g...@hotmail.com wrote: Hi, It seems there is a bug in grompp, which subtracts degrees of freedom for constraints in water also for frozen water molecules. I guess the md.log file reports zero degrees of freedom for your t-coupl group. You can circumvent this issue by putting all your frozen atoms in a separate t-coupling group. Berk
Re: [gmx-users] problem with the size of freeze groups
Dear Berk, I have checked my inputs and tcl scripts that i have used for the selection, i could see that my selection doesn't have any problem. I submitted it again still i am getting the same log file with nrdf 0 for non-freezing group. Please let me know if you want see any of my input files, and help me if you have solution for this problem. Thanks and Regards Srinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.comwrote: Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again. Thanks for your valuable time and kind help. Srinivas. On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess g...@hotmail.com wrote: Hi, Which version of Gromacs are you using? I can't see any issues in the 4.0 code, but some older version might have problems. Berk -- Date: Fri, 26 Feb 2010 12:05:56 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote: That is what I suspected, by I don't know why this is. Are you really sure you made a temperature coupling group that is exactly the freeze group? This first mdp file you mailed had a different group names for the freeze group and the tcoupl groups. Berk -- Date: Fri, 26 Feb 2010 11:53:49 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 + grpopts: (system with 25A) nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 I think some thing is going wrong when the size of freezing group is increased. I don't know whether my understand is correct or not. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote: Ah, but that does not correspond to the mdp options tou mailed. Here there is only one group with 0 degrees of freedom and reference temperature 0. Berk -- Date: Fri, 26 Feb 2010 10:50:13 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org HI Thanks, My log file shows me nrdf: 0 ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote: Hi, Then I have no clue what might be wrong. Have you check nrdf in the log file? Berk -- Date: Fri, 26 Feb 2010 09:54:22 -0500 Subject: Re: [gmx-users] problem with the size of freeze groups From: jampa...@gmail.com To: gmx-users@gromacs.org Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Tmp2 freezedim = Y Y Y
[gmx-users] problem with freezing group size
Dear all, I am sorry for poorly describing my problem about the freezing group size. Here I am giving my question very briefly, can anybody help me please? I would like to know the relation between the size of freezing group and the temperature coupling. when I separate the temperature coupling for freezing and non freezing groups the initial temperature for whole system is showing me zero in the log file, and the non-freezing group is just vibrating not at all moving during the course of simulation. This is true only when I am using large freezing group (freezing group has 26540 atoms and non-freezing group has around 9000 atoms). However if I use small freezing group (freezing group has 7340 atoms and non-freezing group has around 25840 atoms) I am getting log file with initial temperature as 300K, and the non-freezing group is moving well and the diffusion coefficient of solvent is matching with its corresponding value in the bulk (with out freezing). I hope somebody understand my problem now!!! thanks very much. Thanks in advance Srinivas. -- * J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104 Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with the size of freeze groups
Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for MD, and temp coupling is applied for freezing and non freezing waters separately. In case of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 cm2/s (comparable with bulk), but the system with 25 Å radius gives me almost 0 diffusion coefficient. When I open the log file of 25 Å system it shows the initial temperature as zero. Is there any relation between size of freezing group and temperature coupling? How the sphere with 35 Å radius is working fine but not with the radius 25 Å? Can anybody help me? Here is my m.mdp file +++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 150 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp= 300.0 acc_grps= Tmp2 accelerate = 0.1 0.1 0.1 gen_seed= 173529 freezegrps = Freez freezedim = Y Y Y +++ -- * J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104 Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx ** -- 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
