Re: [gmx-users] Viscosity
On 2013-06-01 02:24, Marcelo Vanean wrote: Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. Please give some details about your system and how you did the analysis. Did you use the same energy file with the different gromacs versions? In that case they should give the same result. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] OPLSAA.ff
For example, C* is used in ffbonded.itp, which can be looked up in ffnonbonded as opls_500, which atomtypes.atp reveals as a Trp gamma carbon. Mark On Sat, Jun 1, 2013 at 2:27 AM, Broadbent, Richard richard.broadben...@imperial.ac.uk wrote: The conversion is in ffnonbonded.itp. However, unless you plan to modify the forcefield you shouldn't need this. Richard On 01/06/2013 00:57, Hari Pandey hariche...@yahoo.com wrote: Dear Gromacs users, I am a new user and I have some questions I confused about indexing. in atomtypes.atp clearly we can know the index is for what kind of atom but in ffbondedtype.itp there is different kind of the indexing so I confused how do i pathch the force field . Some are obvious (OH, is oxygen bonden to hydrogen and HO is a hydrogen bonded to oxygen) but definitively I dont know what type of bond makes the carbon atoms like C_2, C_3 or C * Can somebody help me what represents in ffbonded.atp. for example : opls_083 means S in RSR , opls_091 means CH2 in RCH2SR but what type of atoms are C*, C_2, C_3 , CT, CM, CS, LP, CT_2, CT_3, CW, NB etc. could you please provide me idea or list for that if somebody have. Thanks In Oplsaa.ff the indexing is as follows : atomtypes.atp opls_0791.00800 ; H(O) ALCOHOLS JPC,90,1276 (1986) opls_080 15.03500 ; CH3 IN METHANOL JPC,90,1276 (1986) opls_081 14.02700 ; CH2 IN ETHANOLJPC,90,1276 (1986) opls_082 32.06000 ; S IN H2SJPC,90,6379 (1986) opls_083 32.06000 ; S IN RSHJPC,90,6379 (1986) opls_084 32.06000 ; S IN RSRJPC,90,6379 (1986) opls_085 32.06000 ; S IN RSSR JPC,90,6379 (1986) opls_0861.00800 ; H IN H2SJPC,90,6379 (1986) opls_0871.00800 ; H(S) IN RSH JPC,90,6379 (1986) opls_088 15.03500 ; CH3 IN CH3SH JPC,90,6379 (1986) opls_089 14.02700 ; CH2 IN CH3CH2SH JPC,90,6379 (1986) opls_090 15.03500 ; CH3 IN CH3SR JPC,90,6379 (1986) opls_091 14.02700 ; CH2 IN RCH2SR JPC,90,6379 (1986 The ffbonded.itp is as follows ; Some esoteric OPLS atomtypes are not freely available (or depreciated). ; Interaction types involving these have been commented out. [ bondtypes ] ; ij func b0 kb OWHW 10.09572 502080.0 ; For TIP4F Water - wlj 1/98 OWLP 10.01750 753120.0 ; -idem- C*HC 10.10800 284512.0 ; C C3 1 0.15220 265265.6 ; END C_2 C3 10.15220 265265.6 ; END C_3 C3 10.15220 265265.6 ; END C CA 1 0.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97 C_3 CA 10.14900 334720.0 ; wlj 8/97 C CB 10.14190 374049.6 ; GUA C_2 CB 10.14190 374049.6 ; GUA C_3 CB 10.14190 374049.6 ; GUA C CM 1 0.14440 343088.0 ; THY C_2 CM 10.14440 343088.0 ; THY C_3 CM 10.14440 343088.0 ; THY C CS 10.14900 334720.0 ; C_2 CS 10.14900 334720.0 ; C_3 CS 1 0.14900 334720.0 ; C CT 10.15220 265265.6 ; C_2 CT 10.15220 265265.6 ; C_3 CT 10.15220 265265.6 ; C CT_21 0.15220 265265.6 ; AA Calpha C_3 CT_210.15220 265265.6 ; AA C-term NOON 10.12250 460240.0 ; wlj nitro CSCW 10.13670 456892.8 ; wj/nm CSCS 10.14240 392459.2 ; -idem- CSCB 10.14240 392459.2 ; -idem- CS HA 10.10800 307105.6 ; -idem- CUNB 10.13200 343088.0 ; -idem- CUCA 10.14210 392459.2 ; -idem- CU HA 10.10800 307105.6 ; -idem- NANB 10.13490 334720.0 ; -idem- OSNB 10.13990 386601.6 ; -idem- OS CR 10.13570 386601.6 ; -idem- C3C3 10.15260 217568.0 ; Ethane C!C! 10.14600 322168.0 ; wlj C! CS 10.14600 322168.0 ; wlj -- 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 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
[gmx-users] cation-pi interaction
Greeting I'm trying to find the angle between a cation and a benzene cycle from a MD trajectory. I'm really confused is there a tool for such calculations ? because i must find angle using a plan passing by the center of the cycle and vector (from cation to the mass center of the benzene cycle). How can i do it please ?. thanks in advance. -- 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] Vritual Sites and simulation time-step
On Thu, May 30, 2013 at 12:17 PM, James Starlight jmsstarli...@gmail.comwrote: Mark, thanks for advise. As I understood for the usage of virtual sites in typical protein-water system I should (1) define all hydrogens as the virtual atoms (2) increase atom masses of the hydrogens presented in the water, Not applicable if you are using a rigid water model. COOH NH2 OH and SH as well as polar groups (3) make virtual sites for the angles and dihedrals of peptide bond as well as sidechains. Also I've noticed that (1) and (2) can be done with the pdb2gmx with options -vsite and -heavyh respectfully. From this point its not quite clear for me (1) should I make some corrections in topology for dihedrals? In the manual 6.7 I've found some suggestions for the dihedrals of the different functional groups. Generally, use what pdb2gmx will generate and don't worry further. I have heard the thought expressed that the aromatic constructions are not good in practice, but I don't know any details. (2) should I define VSITES for solvent molecules filled into the box by the genbox ? (3) As I understood the inclusion of the VSITES for hydrogens would allow me to increase timestep up to 5-8fs. What possible negative side-effects of the inclusion of VSITES might occur in simulation ? The vsites are generally fine. See paper referenced there for some details. Mark James 2013/5/30 Mark Abraham mark.j.abra...@gmail.com Manual 6.7? On Thu, May 30, 2013 at 7:05 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! In some discussions I've noticed that people told about usage of virtual sites which allow to increase time step of the simulation of such systems. From manual and tutorial its not quite understand for me how with inclusion of such dummy atoms (which can be used to reduce number of atoms of the some solvent-like molecule or to mimic electron pairs in the water for instance) influence on time-step can be achieved ? James -- 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 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 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 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] Vritual Sites and simulation time-step
On Thu, May 30, 2013 at 12:31 PM, James Starlight jmsstarli...@gmail.comwrote: Also some questions about corrections in the mdp besides the time-step file which should be included with the VS. 1) What constrains algorithm should I use ? typically I use ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy At high parallelization, all-bonds becomes limiting, which can be mitigated with changed lincs parameters. See manual. 2) Should I vary tau_t constant assuming that I use SD integrator as the thermostat ( I'm using 2 ps ) ? Don't know. Mark 2013/5/30 James Starlight jmsstarli...@gmail.com Mark, thanks for advise. As I understood for the usage of virtual sites in typical protein-water system I should (1) define all hydrogens as the virtual atoms (2) increase atom masses of the hydrogens presented in the water, COOH NH2 OH and SH as well as polar groups (3) make virtual sites for the angles and dihedrals of peptide bond as well as sidechains. Also I've noticed that (1) and (2) can be done with the pdb2gmx with options -vsite and -heavyh respectfully. From this point its not quite clear for me (1) should I make some corrections in topology for dihedrals? In the manual 6.7 I've found some suggestions for the dihedrals of the different functional groups. (2) should I define VSITES for solvent molecules filled into the box by the genbox ? (3) As I understood the inclusion of the VSITES for hydrogens would allow me to increase timestep up to 5-8fs. What possible negative side-effects of the inclusion of VSITES might occur in simulation ? James 2013/5/30 Mark Abraham mark.j.abra...@gmail.com Manual 6.7? On Thu, May 30, 2013 at 7:05 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! In some discussions I've noticed that people told about usage of virtual sites which allow to increase time step of the simulation of such systems. From manual and tutorial its not quite understand for me how with inclusion of such dummy atoms (which can be used to reduce number of atoms of the some solvent-like molecule or to mimic electron pairs in the water for instance) influence on time-step can be achieved ? James -- 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 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 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 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] Vritual Sites and simulation time-step
On Fri, May 31, 2013 at 5:19 PM, James Starlight jmsstarli...@gmail.comwrote: 3) Also I've already performed small simulation with the time step 5 fs (defining virtual sites by means of pdb2gmx -vsites and introducing heavy hydrogens. I've not observed any errors during my simulation. When I've tried to increase dt up to 7 fs I've obtained warnings according to that I should increase tau_p (from 2 ps with Parinello coupling). How tau_p is relevant to the timestep and when I could obtain more information about such constants ? E.g if i increase tau_p doest it means that I provide weaker coupling to the system with pressure bath ? (higher constant- higher relaxation times ) You're integrating forces calculated at one instant and assuming they are applicable over a finite time period. Obviously this is an approximation, and it gets worse with longer time step. The worse approximation means the sampling is from a shadow Hamiltonian that is even further from the real one. P-R is not very stable if the sampling is not from equilibrium, so probably the change suggested in the warning helps keep P-R working. The absence of the simulation crashing is not a suitable proxy for assuming there are no problems. You should compare observables with those from conservative parameter sets and see whether differences exist. 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/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] nvt T coupling group problem
Hello everyone I have a protein with covalently attached prosthetic group. Now while trying use thermostat I grouped the protein and prosthetic group though an index file asProtein_pro my Tc group is astc-grps= Protein_pro Non-Protein Now issuing the grompp for nvt step, following error is appearing Atom 1076 in multiple T-Coupling groups (1 and 2) This is very obvious that the prosthetic group will be in nonprotein index. The how to couple the prosthetic group and protein together with non protein. Or is it fine to couple a part of protein (prostheic group) with nonprotein. Any suggestion will be highly regarded. -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad -- 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] Re: umbrella sampling for two polymer interaction
Dear Thomas, In AMBER I remember I did once methane-methane interaction, just distance based umbrella sampling. But there I did not provide any direction. So should it not be N N N in Gromacs if I want to allow them freely move in xyz. Sorry am wrong that should be Y Y Y in Gromcacs! for such case regards, On Fri, May 31, 2013 at 10:03 PM, gromacs query gromacsqu...@gmail.comwrote: Dear Thomas, Thanks a lot again for great reply. Please clarify this also, If one uses only 'Y N N' B would only move along the x-axis due to the pull, but could move freely in the yz-plane You never want to use the pull-code and 'pull_dim = N N N' This would mean that there is no force acting between your two groups. Then one could have skipped using the pull-code... So keeping Y N N will allow free movement in yz plane. So if I want A B to move freely in xyz but just keep them separated by some distance with spring const (just like two balloons tied to each other flying in air). Sorry confused. In AMBER I remember I did once methane-methane interaction, just distance based umbrella sampling. But there I did not provide any direction. So should it not be N N N in Gromacs if I want to allow them freely move in xyz. thanks, On Fri, May 31, 2013 at 8:53 PM, Thomas Schlesier schl...@uni-mainz.dewrote: For comments to your questions see below. More general: (somewhat longer than i wanted. Hope you find some answers here) Imagine two interacting particles A and B which are alinged to the x-axis. We take A as the reference group, B as pulled group and put the origin of the umbrella potential on top of B (pull_start=yes). Simulation starts - A and B moves. Pull-code step: From A we calculate the new position of the umbrella potential, this is unequal to B, since B moved and our reference point move. Now we have a force acting on B, 'pull_dim' controls in which directions the force acts. With 'Y Y Y' B is pulled towards the origin of the umbrella potential (and with this to the position it should have relative to A). If one uses only 'Y N N' B would only move along the x-axis due to the pull, but could move freely in the yz-plane. In the end one would get a structure where A and B have the right distance in the x-axis but are miles away from each other in the yz-plane. Now imagine we pull B away from A. Since MD simulations normally separete the movement of the center of mass of the system, it would look like A and B would move away from a middle point. (Interchanging A and B should give the same results). Think in your case (doing umbrella sampling) the mdp-file you suggested would be most appropiate (with 'pull_start=yes' and 'pull_ngroups=1'). This gives you a potential which fixes the distance between the two proteins. One thing you should be aware is that if you restrain the distance in 3d, you have to account for entropic effects (see also the GROMACS manual). If you restrain the system only in one direction, these don't arise. Think this is the reason why one sees some work with umbrella sampling were the restraint works only in one direction. Am 31.05.2013 17:20, schrieb gmx-users-requ...@gromacs.org: Dear Thomas, Thanks a lot for your time and nice explanation. I was not able to get specially the pull_start flag but now its quite clear. I feel sorry, that should be pull_dim = N N N in my case. Also I will be much thankful if you please can help me to make understand following: STOP!!! You never want to use the pull-code and 'pull_dim = N N N' This would mean that there is no force acting between your two groups. Then one could have skipped using the pull-code... 1) If you do a pulling simulation, there can be reason for chosing the groups (protein = reference , ligand = pulled group, since we want to pull it away) This indeed is correct but I am not able to get depth of this. I mean to say lets keep ligand as a reference and protein as pulled group then yes it sounds stupid but I am not able to provide a reason myself why we can not keep ligand as reference and pull protein rather !! Think this setup should also work. For some simple systems i imagine it should give identical results. For complex system i would also think so. But i can't comment on this with actual expirience. The dimer systems which i investigated were symmetric... 2) 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 Better use a reference group - pull_ngroups = 1 You don't want to pull in absolute coordinates, when your system can rotate.. I am not able to understand this part. Can you please provide some example so that it makes easier to understand this Imagine only a single protein which you want to unfold. In an equilibrium simulation the protein can freely rotate in the box. If we use the N-terminus as the reference group and the C-terminus a the pulled group, the
Re: [gmx-users] nvt T coupling group problem
If the rest of your system is just water and ions, couple them separately into another group and include it in your .mdp file. On Sat, Jun 1, 2013 at 2:23 PM, neshat haq neshat...@gmail.com wrote: Hello everyone I have a protein with covalently attached prosthetic group. Now while trying use thermostat I grouped the protein and prosthetic group though an index file asProtein_pro my Tc group is astc-grps= Protein_pro Non-Protein Now issuing the grompp for nvt step, following error is appearing Atom 1076 in multiple T-Coupling groups (1 and 2) This is very obvious that the prosthetic group will be in nonprotein index. The how to couple the prosthetic group and protein together with non protein. Or is it fine to couple a part of protein (prostheic group) with nonprotein. Any suggestion will be highly regarded. -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Vritual Sites and simulation time-step
Thanks for so detailed explanation! I've also forced with the problem of barostat during simulation of my membrane protein with N-H chains ( see adjacent topic). I'll be also very thankful for you suggestion in that case too. James 2013/6/1 Mark Abraham mark.j.abra...@gmail.com On Fri, May 31, 2013 at 5:19 PM, James Starlight jmsstarli...@gmail.com wrote: 3) Also I've already performed small simulation with the time step 5 fs (defining virtual sites by means of pdb2gmx -vsites and introducing heavy hydrogens. I've not observed any errors during my simulation. When I've tried to increase dt up to 7 fs I've obtained warnings according to that I should increase tau_p (from 2 ps with Parinello coupling). How tau_p is relevant to the timestep and when I could obtain more information about such constants ? E.g if i increase tau_p doest it means that I provide weaker coupling to the system with pressure bath ? (higher constant- higher relaxation times ) You're integrating forces calculated at one instant and assuming they are applicable over a finite time period. Obviously this is an approximation, and it gets worse with longer time step. The worse approximation means the sampling is from a shadow Hamiltonian that is even further from the real one. P-R is not very stable if the sampling is not from equilibrium, so probably the change suggested in the warning helps keep P-R working. The absence of the simulation crashing is not a suitable proxy for assuming there are no problems. You should compare observables with those from conservative parameter sets and see whether differences exist. 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/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 * 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 Checkpoint error in gromacs 4.6
Dear Justin Thank you for your previuos reply I am using gromacs 4.6 AMD 8 core processor When I run restart My run from the Checkpoint file using the following error ./mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -append The original run wrote a file called 'CNTPEPRSOLNPT.trr' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend How to solve this error? Thnaks In ADVANCE -- 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] (no subject)
On 2013-06-01 02:24, Marcelo Vanean wrote: Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. -- 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] Re: Nose-Hover chains for membrane protein simulation
I can't think of any instance where nose-hoover chains provides an advantage over nose-hoover in a large system -- all the demonstrations of superiority are in model systems that are not particularly chaotic. As the system gets more chaotic, it matters less. I would go with md, nose-hoover (w/o chains), and Parrinello-Rahman with semiisotropic scaling. On Sat, Jun 1, 2013 at 1:07 AM, James Starlight jmsstarli...@gmail.com wrote: Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK barostat 5ps coupling ) I've observed non-physical behaviour of my system with the constant drift of the protein molecule as the rigid body in the y-z plane Energy Average Err.Est. RMSD Tot-Drift --- Pressure -760.137 --193.776218.059 (bar) From manual I've noticed that MMTK doest not support *semiisotropic scalling. *Doest it means that with the Nose-hover chains and md-vv I should use only weaker coupling during productions runs (I cant use Parinello;s barostat with such options too) Thanks for help James 2013/5/31 James Starlight jmsstarli...@gmail.com Dear Gromacs users! I'd like to perform simulation of the membrane protein in lipid-water system using Nose-Hover with chains. From manual I've found that with such thermostat I should use (1) md-vv integrator (2) MTTK instead of Parinello's batostat and (3) shake instead of LINCS. How doest such options compatible with the simulation of membrane proteins in general ? On what other options should I pay attention during simulation of membrane protein with NH chains ? Thanks for help, James -- 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 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] About Checkpoint error in gromacs 4.6
How about running with -noappend? On 1 Jun 2013, at 13:59, vidhya sankar scvsankar_...@yahoo.com wrote: Dear Justin Thank you for your previuos reply I am using gromacs 4.6 AMD 8 core processor When I run restart My run from the Checkpoint file using the following error ./mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -append The original run wrote a file called 'CNTPEPRSOLNPT.trr' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend How to solve this error? Thnaks In ADVANCE -- 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 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] About Checkpoint error in gromacs 4.6
Respected Erik Marklund, Thank you for your reply When i run with a -noappend option from the checkpoint it runs well but Ooutput files are in Different Names The files Are not merged (are not Continues) ./mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -noappend -- 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] About Checkpoint error in gromacs 4.6
On 6/1/13 9:51 PM, vidhya sankar wrote: Respected Erik Marklund, Thank you for your reply When i run with a -noappend option from the checkpoint it runs well but Ooutput files are in Different Names The files Are not merged (are not Continues) Precisely what -noappend is designed to do. Either you append (and keep the old file names, adding new content to them) or you don't append (and get new files that take up from where the last interval of simulation time left off). -Justin ./mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -noappend -- 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 * 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] OPLS-AA to CHARMM conversion in gromacs ffnonbonded.itp
On 5/31/13 1:18 PM, tarak karmakar wrote: Dear All, I have a little confusion with the non-bonding parameters conversion from OPLS-AA to CHARMM in gromacs. If I see the ffnonbonded.itp in both the cases I get the following numbers OPLS-GROMACS Sigma = 0.1644471 nm Epsilon = (0.875044*4.184) = 3.66118 kJ/mol . CHARMM-GROMACS Sigma = 0.21114299 nm Epsilon = 0.06276 kJ/mol Now, from the charmm27 parameters file I get CHARMM27 Rmin/2 = 1.18500 Ang Epsilon = -0.0150 kcal/mol Converting these charmm parameters to gromacs formate I have to do following conversions Sigma = 2^(5/6) * (Rmin/2) = 2^(5/6) * 1.185 = 2.1114299 Ang = 0.2114299 nm Epsilon = 0.0150 * 4.184 = 0.06276 kJ/mol So, CHARMM (par_water_ions.prm) to charmm(ffnonbonded.itp) is fine. But the problem I'm facing to convert the OPLS(ffnonbonded.itp) to CHARMM(ffnonbonded.itp). Why should they be the same? They're different force fields, so they have different parameters. -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 * 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] viscosity
On 2013-06-01 17:11, Marcelo Vanean wrote: On 2013-06-01 02:24, Marcelo Vanean wrote: Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. Maybe you can post the energy file on that site as well. Have you tried to compute the pressure autocorrelation (using g_energy)? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] About Checkpoint error in gromacs 4.6
Deat Justin Thank you for your Previuos Reply, But When I Run tne the following command with Append Option mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -append I Have got the following error The original run wrote a file called 'CNTPEPRSOLNPT.trr' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend How to Solve this ? But When i Run With -noappend option It run Well But it Produce different File Name files Are not merged (are not Continues) Thanks In Advance -- 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] viscosity
*On 2013-06-01 17:11, Marcelo Vanean wrote: * *On 2013-06-01 02:24, Marcelo Vanean wrote: * *Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. * *I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. * *Maybe you can post the energy file on that site as well. Have you tried to compute the pressure autocorrelation (using g_energy)?* I didn't the pressure autocorrelation. A question: what does this analysis tell me? I posted the energy file here: http://www.4shared.com/file/SSAU1reN/ener.html. -- 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
