Re: [gmx-users] node decomposition' problem
On 7/9/12 4:25 PM, Justin A. Lemkul wrote: On 7/9/12 4:23 PM, Thales Kronenberger wrote: I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: "There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition" I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation The minimum charge group size depends on a whole host of factors: *Edit* "minimum domain decomposition cell" - I don't know where "charge group" came from... http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm The large size you have obtained indicates there are likely problems with the .mdp file, topology, or both. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] node decomposition' problem
On 7/9/12 4:23 PM, Thales Kronenberger wrote: I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: "There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition" I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation The minimum charge group size depends on a whole host of factors: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm The large size you have obtained indicates there are likely problems with the .mdp file, topology, or both. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] node decomposition' problem
I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: "There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition" I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: DNA simulations
On 7/9/12 4:07 PM, SatyaK wrote: Hello, I followed below steps using VMD and GROMACS but something went wrong in using GROMACS which I am not able to figure out. Appreciate your help. 1. editconf -f initialfile.pdb -o initialfile.gro -d 0.2 2. VMD: within 5 of nucleic $sel writepdb initialfile_updated.pdb $sel delete (initialfile_updated.pdb has only those molecules that are at a distance of 5A) 3. I used GROMACS to convert back to .gro:editconf -f initialfile_updated.pdb -o initialfile_updated.gro -d 0.2 The coordinates in ininitialfile.gro and initialfile_updared.gro are different. I quite don't understand the reason for the same. You are resetting the box by invoking the -d option with editconf. If initialfile.gro had all the original atoms and initialfile_updated.gro has significantly fewer (due to the selection made in VMD), then the size associated with the system is much smaller. Using -d re-centers the system within the defined box, thus shifting the coordinates. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] Re: DNA simulations
Hello, I followed below steps using VMD and GROMACS but something went wrong in using GROMACS which I am not able to figure out. Appreciate your help. 1. editconf -f initialfile.pdb -o initialfile.gro -d 0.2 2. VMD: within 5 of nucleic $sel writepdb initialfile_updated.pdb $sel delete (initialfile_updated.pdb has only those molecules that are at a distance of 5A) 3. I used GROMACS to convert back to .gro:editconf -f initialfile_updated.pdb -o initialfile_updated.gro -d 0.2 The coordinates in ininitialfile.gro and initialfile_updared.gro are different. I quite don't understand the reason for the same. Thanks, Satya. -- View this message in context: http://gromacs.5086.n6.nabble.com/DNA-simulations-tp4998988p4999250.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] water model
For CHARMM the typical water model is TIP3P, although I tend to use TIPS3P since it's been reported on the mailing list to give better interactions with bilayers. (Also easier to pass by picky reviewers at the expense of ns/day, obviously). The following thread may be helpful too: http://lists.gromacs.org/pipermail/gmx-users/2010-September/053960.html On 2012-07-09 10:49:57AM -0700, Shima Arasteh wrote: > > > Dear gmx friends, > > Is there the best water model for each force fields? Which options are > supposed to be noticed in applying the best water model. > I need to tell you that I apply C36 in my simulations. > > Thanks in advance. > > Sincerely, > Shima > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] water model
Dear gmx friends, Is there the best water model for each force fields? Which options are supposed to be noticed in applying the best water model. I need to tell you that I apply C36 in my simulations. Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] force field parametrs for Mn2+
sorry it's my mistake . thanks a lot for the reply. On Mon, Jul 9, 2012 at 10:55 PM, Justin A. Lemkul wrote: > > > On 7/9/12 1:21 PM, tarak karmakar wrote: >> >> Oh !! nice work >> Thanks a lot for the quick reply. But I'm very sorry to inform you >> that whichever table [supplementary table S4] you are specifying in >> the supporting info, I couldn't find anywhere. So, may be I'm finding >> my way in wrong track. Can you please provide me the link and / the >> table containing the parameters for the Manganese ? > > > It's on p. 11 of the supplement. > > http://onlinelibrary.wiley.com/store/10.1002/anie.201202032/asset/supinfo/anie_201202032_sm_miscellaneous_information.pdf?v=1&s=cff1986017d1843da85eb75dbd174c8e11727dc8 > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * 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 -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] force field parametrs for Mn2+
On 7/9/12 1:21 PM, tarak karmakar wrote: Oh !! nice work Thanks a lot for the quick reply. But I'm very sorry to inform you that whichever table [supplementary table S4] you are specifying in the supporting info, I couldn't find anywhere. So, may be I'm finding my way in wrong track. Can you please provide me the link and / the table containing the parameters for the Manganese ? It's on p. 11 of the supplement. http://onlinelibrary.wiley.com/store/10.1002/anie.201202032/asset/supinfo/anie_201202032_sm_miscellaneous_information.pdf?v=1&s=cff1986017d1843da85eb75dbd174c8e11727dc8 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] force field parametrs for Mn2+
Oh !! nice work Thanks a lot for the quick reply. But I'm very sorry to inform you that whichever table [supplementary table S4] you are specifying in the supporting info, I couldn't find anywhere. So, may be I'm finding my way in wrong track. Can you please provide me the link and / the table containing the parameters for the Manganese ? Thanks in advance. Tarak On Mon, Jul 9, 2012 at 4:58 PM, andrea spitaleri wrote: > Hi, > we published recently a paper where we determined the oplsaa parameters for > Mn2+; > have look to (supp mat): > > http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/abstract > > > hope it helps > > > > On 07/09/2012 12:21 PM, tarak karmakar wrote: >> >> Dear All, >> >> >> Please suggest me any paper/article that contains force field >> parameters for Mn 2+ . >> >> Thanks >> > > -- > - > Andrea Spitaleri PhD > Dulbecco Telethon Institute c/o Raffaele Scientific Institute > Biomolecular NMR Laboratory Dibit2 Basilica 3A2 > Via Olgettina 58 > 20132 Milano > Italy > Tel: 0039-0226434348 > Fax: 0039-0226434153 > http://sites.google.com/site/andreaspitaleri/ > http://www.linkedin.com/in/andreaspitaleri > - > -- > LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. > AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153 > info:www.5xmi...@hsr.it - www.5xmille.org > > Disclaimer added by CodeTwo Exchange Rules 2007 > http://www.codetwo.com > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] About lipid simulation...
Hi Gromacs friends, I am very novice to the lipid simulation study.. My problem may be very simple, But very imp to me to know it. I am trying to reproduced the result of article ¨Antimicrobial peptide in Action¨ Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q As per article they used two conditions, 1. Stress free ( Lateral Tension = 0) 2. Stress condition ( Lateral tension = 20 mNm/m) parameter for simulation as follow, Weakly coupled temp 323 k ( Coupling time = 0.1) Weakly coupled press ( Coupling time = 0.5 Compressibility 5 e-5 bar -1) Keep the P|| ( lateral press ) and Pz( Perpendicular press ) same P|| = Pz = 1 , Result will be stress free bilayer ( Lateral Tension = 0). For other condition of P|| = -30 Pz = 1 , result in a lateral tension of 20 mNm/m for stress free condition I made following npt.mdp ; Temperature coupling is on tcoupl= Berendsen; More accurate thermostat tc-grps= Protein DPPCSOL_CL; three coupling groups - more accurate tau_t= 0.10.10.1; time constant, in ps ref_t= 323 323323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Berendsen; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 0.5; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1 And for stress condition I made the following npt.mdp ; Temperature coupling is on tcoupl= Berendsen; More accurate thermostat tc-grps= Protein DPPCSOL_CL; three coupling groups - more accurate tau_t= 0.10.10.1; time constant, in ps ref_t= 323 323323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Berendsen; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 0.5; time constant, in ps ref_p= -30.01.0; reference pressure, x-y, z (in bar) compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1 Please help to make right npt.mdp from above mention parameter. I read the Gromacs manual for 4.5.4, Section 3.4 page no 33, Surface tension coupling work with only Berendsen Press coupling. Please , would you tell me how to calculate lateral surface tension from P|| ( lateral press ) and Pz( Perpendicular press ) ??? ( Why to say P|| = -30 Pz = 1 , will give the teral tension of 20 mNm/m ???) Please give me the valuable suggestion in these regard Thank you in advance. Have a nice Day. With best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Problems with solvation in SW (water shell model)
Hello, I'm trying to solvate an OPLSAA methanol molecule in polarizable water shell. Initially I generated a box of pure water using the TIP5P box available in gromacs 4.5. I simulated pure water and I got all the bulk properties in agreement with published results for SW water. In sequence, I used genbox to add the SW water in a 3x3x3 box with a molecule of methanol. By using grompp I received the following error message when I tried minimization Fatal error: Syntax error - File sw.itp, line 36 Last line read: 'LJ Geometric' Found a second defaults directive. Following a suggestion I found on the gmx-forum I commented the following lines of the sw.itp file. [ defaults ] LJ Geometric Done it, I got pre-process the files, but mdrun gave me the segmentation fault: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps= 5000 Segmentation fault: 11-02 nm, Epot= nan Fmax= 1.61425e+04, atom= 2380 Besides I can not minimize the solution, I also noticed that after I have commented the lines of the file sw.itp, I did not get back to simulate the pure water again. Anyone have any tips on how I could solve this problem? Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] error in mdrun
I already decrease it to 0.002 as you said and then there comes this error I wrote to you. Now It try it with 0.001. It is still running. Thank you for your answer. Eva > > > On 7/9/12 9:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> With the mentioned below options I get the following error: >> >> Fatal error: >> 1 particles communicated to PME node 1 are more than 2/3 times the >> cut-off >> out of the domain decomposition cell of their charge group in dimension >> x. >> This usually means that your system is not well equilibrated. >> >> >> But it does not occur immediatly but only at step >> >> Step 695, time 1.39 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 2.011725, max 78.611298 (between atoms 3778 and 3781) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 3782 3785 92.21.3061 0.2785 0.1090 >> 3782 3784 93.00.1055 0.2552 0.1090 >> 3782 3783 91.00.1062 0.3086 0.1090 >> 3204 3206 89.60.1449 1.0256 0.1449 >> 3204 3205 89.70.1010 0.9949 0.1010 >> >> >> Is there something wrong with my temperature coupling? >> > > I doubt it. Decrease your timestep (as I've said twice now) and try again > with > something sensible for dt. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Reg dimers
Thanks a lot Justin On Mon, Jul 9, 2012 at 7:21 PM, Justin A. Lemkul wrote: > > > On 7/9/12 9:48 AM, Ramya LN wrote: >> >> Dear all, >> I have done protein-ligand dynamics.I got the final gro file.When >> converted to PDB, i observed that my active site has ligand but two >> chains of teh protein got separated. What might be the reason for >> this?should i consider this as an error in my simulation???kindly help >> me in this regard. >> > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * 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 -- Ramya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Reg dimers
On 7/9/12 9:48 AM, Ramya LN wrote: Dear all, I have done protein-ligand dynamics.I got the final gro file.When converted to PDB, i observed that my active site has ligand but two chains of teh protein got separated. What might be the reason for this?should i consider this as an error in my simulation???kindly help me in this regard. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] error in mdrun
On 7/9/12 9:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: With the mentioned below options I get the following error: Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. But it does not occur immediatly but only at step Step 695, time 1.39 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.011725, max 78.611298 (between atoms 3778 and 3781) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3782 3785 92.21.3061 0.2785 0.1090 3782 3784 93.00.1055 0.2552 0.1090 3782 3783 91.00.1062 0.3086 0.1090 3204 3206 89.60.1449 1.0256 0.1449 3204 3205 89.70.1010 0.9949 0.1010 Is there something wrong with my temperature coupling? I doubt it. Decrease your timestep (as I've said twice now) and try again with something sensible for dt. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] Reg dimers
Dear all, I have done protein-ligand dynamics.I got the final gro file.When converted to PDB, i observed that my active site has ligand but two chains of teh protein got separated. What might be the reason for this?should i consider this as an error in my simulation???kindly help me in this regard. Thanks -- Ramya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] error in mdrun
With the mentioned below options I get the following error: Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. But it does not occur immediatly but only at step Step 695, time 1.39 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.011725, max 78.611298 (between atoms 3778 and 3781) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3782 3785 92.21.3061 0.2785 0.1090 3782 3784 93.00.1055 0.2552 0.1090 3782 3783 91.00.1062 0.3086 0.1090 3204 3206 89.60.1449 1.0256 0.1449 3204 3205 89.70.1010 0.9949 0.1010 Is there something wrong with my temperature coupling? Thank you, Eva > Hi Justin, > okey then I will try it with this timestep. > No it is not my goal to do a NVE. I already had temperature coupling > options in my .mdp file but on the blowing up side was written "you are > using inappropriate temperature coupling" so I thought that that might be > the reason and deleted it from my .mdp file. > > I had the following temperature coupling options: > > tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 298 298 > pcoupl = no > > > > Thank you for your answer. > Eva > >> >> >> On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >>> Hi everybody, >>> I want to do a md for a protein with a membrane around it. >>> I already minimised the energy of the protein. >>> >>> >>> >>> Output of the minimization: >>> >>> ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, >>> atom= 1653 >>> Stepsize too small, or no change in energy. >>> Converged to machine precision, >>> but not to the requested precision Fmax < 10 >>> >>> Double precision normally gives you higher accuracy. >>> You might need to increase your constraint accuracy, or turn >>> off constraints alltogether (set constraints = none in mdp file) >>> >>> writing lowest energy coordinates. >>> >>> >>> Steepest Descents converged to machine precision in 813 steps, >>> but did not reach the requested Fmax < 10. >>> Potential Energy = -7.5928356e+05 >>> Maximum force = 3.6197971e+02 on atom 1653 >>> Norm of force = 2.6517429e+00 >>> >>> >>> >>> >>> >>> In my eyes this output was okey so I went on with the md. >>> And here I get the error: >>> >>> Fatal error: >>> A charge group moved too far between two domain decomposition steps >>> This usually means that your system is not well equilibrated >>> >>> >>> >>> >>> I already read the error page for this error and also the blowing up >>> page >>> but I still do not know what to do now. >>> >>> My .mdp file for the md runs looks like this: >>> >>> define = -DPOSRES >>> integrator = md >>> dt = 0.005 >> >> This timestep is huge. Even with constraints, you probably can't exceed >> 2 >> fs >> stably (0.002 ps). >> >>> nsteps = 2000 >>> nstxout = 0 >>> nstvout = 0 >>> nstfout = 0 >>> nstlog = 1000 >>> nstxtcout = 0 >>> nstenergy = 5 >>> energygrps = Protein Non-Protein >>> nstcalcenergy = 5 >>> nstlist = 10 >>> ns-type = Grid >>> pbc = xyz >>> rlist = 0.9 >>> coulombtype = PME >>> rcoulomb= 0.9 >>> rvdw= 0.9 >>> fourierspacing = 0.12 >>> pme_order = 4 >>> ewald_rtol = 1e-5 >>> gen_vel = yes >>> gen_temp= 200.0 >>> gen_seed= >>> constraints = all-bonds >>> >>> >>> Are here any optinos which can cause the error? >>> >> >> In the absence of temperature and/or pressure coupling, the ensemble >> you're >> trying to simulate is NVE, which is very tricky to get stabilized. >> >> http://www.gromacs.org/Documentation/Terminology/NVE >> >> If you're not going for an NVE ensemble, you need several adjustments in >> the >> .mdp file. See any basic tutorial for examples of how to simulate other >> ensembles, if this is your goal. >> >> -Justin >> >> -- >> >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> 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 >> * Only plain text messages are allowed! >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the l
Re: [gmx-users] error in mdrun
On 7/9/12 9:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, okey then I will try it with this timestep. No it is not my goal to do a NVE. I already had temperature coupling options in my .mdp file but on the blowing up side was written "you are using inappropriate temperature coupling" so I thought that that might be the reason and deleted it from my .mdp file. Temperature coupling in itself is not the source of the problem, but what is stated on the wiki is that inappropriate use of it can lead to instability. The settings below look fine. I think your biggest problem is the large timestep. -Justin I had the following temperature coupling options: tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no Thank you for your answer. Eva On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to do a md for a protein with a membrane around it. I already minimised the energy of the protein. Output of the minimization: ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, atom= 1653 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 813 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.5928356e+05 Maximum force = 3.6197971e+02 on atom 1653 Norm of force = 2.6517429e+00 In my eyes this output was okey so I went on with the md. And here I get the error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I already read the error page for this error and also the blowing up page but I still do not know what to do now. My .mdp file for the md runs looks like this: define = -DPOSRES integrator = md dt = 0.005 This timestep is huge. Even with constraints, you probably can't exceed 2 fs stably (0.002 ps). nsteps = 2000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 0 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds Are here any optinos which can cause the error? In the absence of temperature and/or pressure coupling, the ensemble you're trying to simulate is NVE, which is very tricky to get stabilized. http://www.gromacs.org/Documentation/Terminology/NVE If you're not going for an NVE ensemble, you need several adjustments in the .mdp file. See any basic tutorial for examples of how to simulate other ensembles, if this is your goal. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] error in mdrun
Hi Justin, okey then I will try it with this timestep. No it is not my goal to do a NVE. I already had temperature coupling options in my .mdp file but on the blowing up side was written "you are using inappropriate temperature coupling" so I thought that that might be the reason and deleted it from my .mdp file. I had the following temperature coupling options: tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no Thank you for your answer. Eva > > > On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I want to do a md for a protein with a membrane around it. >> I already minimised the energy of the protein. >> >> >> >> Output of the minimization: >> >> ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, >> atom= 1653 >> Stepsize too small, or no change in energy. >> Converged to machine precision, >> but not to the requested precision Fmax < 10 >> >> Double precision normally gives you higher accuracy. >> You might need to increase your constraint accuracy, or turn >> off constraints alltogether (set constraints = none in mdp file) >> >> writing lowest energy coordinates. >> >> >> Steepest Descents converged to machine precision in 813 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -7.5928356e+05 >> Maximum force = 3.6197971e+02 on atom 1653 >> Norm of force = 2.6517429e+00 >> >> >> >> >> >> In my eyes this output was okey so I went on with the md. >> And here I get the error: >> >> Fatal error: >> A charge group moved too far between two domain decomposition steps >> This usually means that your system is not well equilibrated >> >> >> >> >> I already read the error page for this error and also the blowing up >> page >> but I still do not know what to do now. >> >> My .mdp file for the md runs looks like this: >> >> define = -DPOSRES >> integrator = md >> dt = 0.005 > > This timestep is huge. Even with constraints, you probably can't exceed 2 > fs > stably (0.002 ps). > >> nsteps = 2000 >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstxtcout = 0 >> nstenergy = 5 >> energygrps = Protein Non-Protein >> nstcalcenergy = 5 >> nstlist = 10 >> ns-type = Grid >> pbc = xyz >> rlist = 0.9 >> coulombtype = PME >> rcoulomb= 0.9 >> rvdw= 0.9 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> gen_vel = yes >> gen_temp= 200.0 >> gen_seed= >> constraints = all-bonds >> >> >> Are here any optinos which can cause the error? >> > > In the absence of temperature and/or pressure coupling, the ensemble > you're > trying to simulate is NVE, which is very tricky to get stabilized. > > http://www.gromacs.org/Documentation/Terminology/NVE > > If you're not going for an NVE ensemble, you need several adjustments in > the > .mdp file. See any basic tutorial for examples of how to simulate other > ensembles, if this is your goal. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] error in mdrun
On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to do a md for a protein with a membrane around it. I already minimised the energy of the protein. Output of the minimization: ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, atom= 1653 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 813 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.5928356e+05 Maximum force = 3.6197971e+02 on atom 1653 Norm of force = 2.6517429e+00 In my eyes this output was okey so I went on with the md. And here I get the error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I already read the error page for this error and also the blowing up page but I still do not know what to do now. My .mdp file for the md runs looks like this: define = -DPOSRES integrator = md dt = 0.005 This timestep is huge. Even with constraints, you probably can't exceed 2 fs stably (0.002 ps). nsteps = 2000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 0 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds Are here any optinos which can cause the error? In the absence of temperature and/or pressure coupling, the ensemble you're trying to simulate is NVE, which is very tricky to get stabilized. http://www.gromacs.org/Documentation/Terminology/NVE If you're not going for an NVE ensemble, you need several adjustments in the .mdp file. See any basic tutorial for examples of how to simulate other ensembles, if this is your goal. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] error in mdrun (2)
When I run the md run again I get still the already mentioned error and additionally this one: Fatal error: 66 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. I really don't know how to equilibrate it better. Thank you, Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] error in mdrun
Hi everybody, I want to do a md for a protein with a membrane around it. I already minimised the energy of the protein. Output of the minimization: ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, atom= 1653 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 813 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.5928356e+05 Maximum force = 3.6197971e+02 on atom 1653 Norm of force = 2.6517429e+00 In my eyes this output was okey so I went on with the md. And here I get the error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I already read the error page for this error and also the blowing up page but I still do not know what to do now. My .mdp file for the md runs looks like this: define = -DPOSRES integrator = md dt = 0.005 nsteps = 2000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 0 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp= 200.0 gen_seed= constraints = all-bonds Are here any optinos which can cause the error? Bests, Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] define a new residue
Hi :) I got the parameters of the first 3 residues of the peptide and when I got 0.008e for total charge of the first 2 residues ( formyl and valine). It is expected to be zero. Is the 0.008e acceptable? Or I look for an other way to get the correct parameters and charges? Thaankks! :) Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Monday, July 9, 2012 12:35 AM Subject: Re: [gmx-users] define a new residue On 7/8/12 12:43 PM, Shima Arasteh wrote: > OK. > What about generating an output file through CGenFF by the first 3 residues > of the protein, rather thn the first 2 (formyl+valine)? > > Maybe. Try it and see, rather than waiting a few hours for someone to get around to replying :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] force field parametrs for Mn2+
Hi, we published recently a paper where we determined the oplsaa parameters for Mn2+; have look to (supp mat): http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/abstract hope it helps On 07/09/2012 12:21 PM, tarak karmakar wrote: Dear All, Please suggest me any paper/article that contains force field parameters for Mn 2+ . Thanks -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - -- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153 info:www.5xmi...@hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] large radius problem
On 7/9/12 7:09 AM, siddhant jain wrote: I was performing simulations on urea unfolding of protein. I performed one set of simulation for 50 ns with a velocity (set by gen_seed) and it went fine. Now when I am doing simulation using a different gen_seed from 10 to 20 ns many long bonds are formed. I could visualize them in vmd. Subsequently rmsd and radius of gyration plots also show the large change. But, energy is almost constant during the whole time period. Also after 20 ns this problem goes by itself and all bonds become normal. Why it could be so and how could I correct it. These bonds are so long that radius of gyration changes from 1.2 nm to 3.5 nm. That sounds like a PBC issue to me. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] large radius problem
I was performing simulations on urea unfolding of protein. I performed one set of simulation for 50 ns with a velocity (set by gen_seed) and it went fine. Now when I am doing simulation using a different gen_seed from 10 to 20 ns many long bonds are formed. I could visualize them in vmd. Subsequently rmsd and radius of gyration plots also show the large change. But, energy is almost constant during the whole time period. Also after 20 ns this problem goes by itself and all bonds become normal. Why it could be so and how could I correct it. These bonds are so long that radius of gyration changes from 1.2 nm to 3.5 nm. Thanking all in advance Siddhant -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Peptide folding simulation
On 7/9/12 12:02 AM, bharat gupta wrote: Hi, I have been trying to study folding of a peptide 24 residues long. I did a simulation of 50 ns with explicit solvent, CHARMM FF, but I was not able to find even a single folding event. Then I decided use explicit solvent for simulation and I again simulated the peptide for 100 ns . This time again I ended with no folding events. I know that in case of explicit solvent , a 50ns simulation time is not enough to observe anything. But I did it to see the initial behavior of the peptide in water. In take many random like conformation but doesnot fold into a desired beta-hairpin. For the explicit solvent simulation, I followed the lysozyme tutorial parameters. You shouldn't. The .mdp settings are appropriate for OPLS-AA, not CHARMM. For implicit solvent simulation, I used the following parameters for Energy minimization : define = -DFLEXIBLE constraints = none integrator = steep dt = 0.001; ps nsteps = 3 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = Protein optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 For MD I used the following : - define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 10 ; 10 ps = 100 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 300 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 So, finally I want to know where have I gone in my simulation experiments, both implicit and explicit ?? ... Please reply . What evidence do you have that you should expect to see a folding event in such a short time? Most people will use more extensive sampling methods like REMD to observe peptide folding. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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.
[gmx-users] force field parametrs for Mn2+
Dear All, Please suggest me any paper/article that contains force field parameters for Mn 2+ . Thanks -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Peptide folding simulation
Hi To see folding events in your (very) long peptide in explicit solvent, without doing long MD (> 100 ns), you will need to use more complex MD approach such as REMD or metadynamics. REMD is implemented in gromacs, but for the latter one, you can use plumed with GROMACS. See for example http://www.plumed-code.org/ HTH Stephane -- Hi, I have been trying to study folding of a peptide 24 residues long. I did a simulation of 50 ns with explicit solvent, CHARMM FF, but I was not able to find even a single folding event. Then I decided use explicit solvent for simulation and I again simulated the peptide for 100 ns . This time again I ended with no folding events. I know that in case of explicit solvent , a 50ns simulation time is not enough to observe anything. But I did it to see the initial behavior of the peptide in water. In take many random like conformation but doesnot fold into a desired beta-hairpin. For the explicit solvent simulation, I followed the lysozyme tutorial parameters. For implicit solvent simulation, I used the following parameters for Energy minimization : define = -DFLEXIBLE constraints = none integrator = steep dt = 0.001; ps nsteps = 3 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = Protein optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 For MD I used the following : - define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = none integrator = md dt = 0.001 ; ps nsteps = 10 ; 10 ps = 100 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 300 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 So, finally I want to know where have I gone in my simulation experiments, both implicit and explicit ?? ... Please reply . BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] About lipid simulation npt.mdp
Hi Gromacs friends, I am trying to reproduced the result of article ¨Antimicrobial peptide in Action¨ Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q As per article they used two conditions, 1. Stress free ( Lateral Tension = 0) 2. Stress condition ( Lateral tension = 20 mNm/m) parameter for simulation as follow, Weakly coupled temp 323 k ( Coupling time = 0.1) Weakly coupled press ( Coupling time = 0.5 Compressibility 5 e-5 bar -1) Keep the P|| ( lateral press ) and Pz( Perpendicular press ) same P|| = Pz = 1 , Result will be stress free bilayer ( Lateral Tension = 0). For other condition of P|| = -30 Pz = 1 , result in a lateral tension of 20 mNm/m for stress free condition I made following npt.mdp ; Temperature coupling is on tcoupl= Berendsen; More accurate thermostat tc-grps= Protein DPPCSOL_CL; three coupling groups - more accurate tau_t= 0.10.10.1; time constant, in ps ref_t= 323 323323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Berendsen; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 0.5; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1 And for stress condition I made the following npt.mdp ; Temperature coupling is on tcoupl= Berendsen; More accurate thermostat tc-grps= Protein DPPCSOL_CL; three coupling groups - more accurate tau_t= 0.10.10.1; time constant, in ps ref_t= 323 323323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Berendsen; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 0.5; time constant, in ps ref_p= -30.01.0; reference pressure, x-y, z (in bar) compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1 Please help to make right npt.mdp from above mention parameter. I read the Gromacs manual for 4.5.4, Section 3.4 page no 33, Surface tension coupling work with only Berendsen Press coupling. Please , would you tell me how to calculate lateral surface tension from P|| ( lateral press ) and Pz( Perpendicular press ) ??? ( Why to say P|| = -30 Pz = 1 , will give the teral tension of 20 mNm/m ???) Please give me the valuable suggestion in these regard Thank you in advance. Have a nice Day. With best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] specifying the direction of Pull in US
If you want to pull along a vector which connects to groups, the easiest way is to run 'g_dist' over your starting *.gro file. this measures the distance and the vector connecting both groups. From GROMACS-4.0.x you don't need to normalise the vector. So you can directly use this vector. greetings thomas Thanks for ur suggestion Justin, I'm facing trouble in setting that vector, actually I cant figure out how can i set up a vector. Is there any easier way with which i can set up a vector. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Fast Question on g_msd
Both behaviours are possible. Check the -mol option. Javier El 08/07/12 18:30, Ivan Gladich escribió: Dear all I am running a simulation of water slab, i.e. a water system with two air/vacuum interface, using a 5 site water model. I am doing a simple test calculating the water diffusivity by mean square displacement in different regions of my water slab. In order to do, I created an index that contains all the atoms of the water molecules that belong to a certain region using g_select g_select -select " all and same residue as (y>2.5 and y<12.5)" -on select_index.ndx At the end, my select_index.ndx contains all the atoms of all the water molecules that are between 2.5 and 12.5 nm [all] 1 2 3 4 5 11 12 13 14 15 . After that, I calculate the diffusivity of all the waters that belong to this region. g_msd -n select_index.ndx -s topol.tpr I have a silly question. 1) Does g_msd calculate the means square displacement of all the atom that are select_index.ndx (and then it takes the average of all of them)? OR 2)does g_msd read the topol.tpr, recognize that the atoms in select_index.ndx belong to specific water molecules and so, it calculate the msd based on the displacement of the center of mass of each water molecule (and then it takes the average)? Sorry, I tried to find something in the archive but I was able (or lucky) to find something. Thanks for any possible help Ivan - -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] error in grompp
Hi Justin, thank you very much for your help!! > > > On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> thank you for your answer. >> >> Now I tried it with two different restraint .itp files. One for the >> protein and one for the dummy atoms. >> But still it doesn't work. Now the error is: >> >> [ file posre_memb.itp, line 5 ]: >> Atom index (4942) in position_restraints out of bounds (1-1). >> This probably means that you have inserted topology section >> "position_restraints" >> in a part belonging to a different molecule than you intended to. >> In that case move the "position_restraints" section to the right >> molecule. >> >> >> But I think I included it the right way: >> >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Include water topology >> #include "amber03.ff/tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcxfcyfcz >> 11 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "amber03.ff/ions.itp" >> >> #include "amber03.ff/dum.itp" >> #ifdef POSRES >> #include "posre_memb.itp" >> #endif >> >> >> >> In my coordiate file the difference between them look like this: >> >> 313LEU HD23 4938 3.813 4.505 3.308 >>313LEU C 4939 3.435 4.335 3.190 >>313LEUOC1 4940 3.429 4.330 3.090 >>313LEUOC2 4941 3.337 4.305 3.259 >>314DUMDUM 4942 1.996 2.371 6.171 >>314DUMDUM 4943 1.996 2.371 6.271 >>314DUMDUM 4944 1.996 2.471 6.171 >>314DUMDUM 4945 1.996 2.471 6.271 >> >> >> my restraint file for the protein looks like this: >> >> >> ; position restraints for Protein-H of GROup of MAchos and Cynical >> Suckers >> >> [ position_restraints ] >> ; i funct fcxfcyfcz >> 11 1000 1000 1000 >> 41 1000 1000 1000 >> 71 1000 1000 1000 >>101 1000 1000 1000 >>131 1000 1000 1000 >> >> >> and my restraint file for the dummy atoms look like this: >> >> ; position restraints for Protein-H of GROup of MAchos and Cynical >> Suckers >> >> [ position_restraints ] >> ; i funct fcxfcyfcz >> 49421 1000 1000 1000 >> 49431 1000 1000 1000 >> 49441 1000 1000 1000 >> 49451 1000 1000 1000 >> >> >> What is wrong? >> > > Atom numbering is done per [moleculetype] and has nothing to do with the > atom > numbers in the coordinate file. If you have a one-atom dummy > [moleculetype], > then the only valid content of posre_memb.itp is: > > [ position_restraints ] > ; i funct fcxfcyfcz > 11 1000 1000 1000 > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 > * Only plain text messages are allowed! > * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
