[gmx-users] error in umbralla sampling step 6
Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：Justin Lemkul 发送时间：2013年10月27日(星期日) 20:27 收件人：gromacs 主 题：Re: 答复: [gmx-users] error in umbralla sampling step 6 Please keep the discussion on the list. On 10/27/13 5:09 AM, sunyeping wrote: > Dear professor Lemkul, > > For warning 1: > I use the npt_umbrella.mdp file you provided in step 6 in the umbralla > sampling > tutorial. You told us to start by running a brief NPT equilibration in each > window using this mdp file. If Parrinello-Rahman pressure coupling should be > used, why did you put it in the mdp file? > I know the tutorial system is robust enough that it won't matter. That is not necessarily true for whatever other system you come up with. Be careful when extrapolating something that works in a tutorial with something that is untested. The general logic is the same (you need to equilibrate for a little while first), but you have to think a bit about the proper settings. There is also no guarantee that the length of time I set in the tutorial simulation processes (equilibration, SMD, and umbrella sampling) will necessarily be sufficient for whatever you're doing. > For warning 2: > I check the gro files using vmd but I cann't find any molecule broken? How > can I > find the brroken molecule? The only way to find them is to look. I have no special advice for this. > I add -pbc whole option to the trjconv as following: > > trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep -pbc whole > > then It seems that the problemis solved. Is that a correct wayyou mean to > solve the problem? > Then clearly something was broken across PBC, which means there is no real problem. -JustinIn case that something was broken across PBC, why there is no real problem? Do you mean molecule breaking will not affect the simulation result? -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] error in umbralla sampling step 6
Dear gromacs user, I am doing umbralla sampling on a protein-ligand system following the gromacs umbralla sampling turial. It seems that the first five steps go well, and I select 23 gro files as the starting configurations of adjacent umbrella sampling windows. However when I use grompp to generate tpr files for these individual configurations as following: grompp -f npt_umbrella.mdp -c conf86.gro -p topol.top -n index.ndx -o npt86.tprI get the following notes, warning and error information:NOTE 1 [file npt_umbrella.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file npt_umbrella.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file npt_umbrella.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. ...Largest charge group radii for Van der Waals: 16.306, 16.297 nm Largest charge group radii for Coulomb: 16.306, 16.297 nm WARNING 2 [file npt_umbrella.mdp]: The sum of the two largest charge group radii (32.603355) is larger than rlist (1.40) Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Discussion aout warring 2 on the mail-list points out that the error that cause warning 2 will impact the results and lead to artifacts. I cann't understand why the warning occurs here, because it didn't appear when I use grompp in the my previous steps. Could you explain why it occur in this step? Will it really affect umbralla sampling? Can I use the -maxwarn option to ignore it? Best Regards,Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 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] two warnings in umbralla sampling step 6
Dear gromacs user, I am doing umbralla sampling on a protein-ligand system following the gromacs umbralla sampling turial. It seems that the first five steps go well, and I select 23 gro files as the starting configurations of adjacent umbrella sampling windows. However when I use grompp to generate tpr files for these individual configurations as following: grompp -f npt_umbrella.mdp -c conf86.gro -p topol.top -n index.ndx -o npt86.tprI get the following notes, warning and error information:NOTE 1 [file npt_umbrella.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file npt_umbrella.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file npt_umbrella.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. ...Largest charge group radii for Van der Waals: 16.306, 16.297 nm Largest charge group radii for Coulomb: 16.306, 16.297 nm WARNING 2 [file npt_umbrella.mdp]: The sum of the two largest charge group radii (32.603355) is larger than rlist (1.40) Fatal error: Too many warnings (2), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Discussion aout warring 2 on the mail-list points out that the error that cause warning 2 will impact the results and lead to artifacts. I cann't understand why the warning occurs here, because it didn't appear when I use grompp in the my previous steps. Could you explain why it occur in this step? Will it really affect umbralla sampling? Can I use the -maxwarn option to ignore it? Best Regards, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 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] The box of umbrella sampling
Dear gromacs users, I am studying gromacs umbralla sampling. I want to pull a lingand out of its binding pocket in a protein. By observing the ligand-protein complex, I think I should pull the ligand along a direction which is not parallel to the x, y or z axis so as to prevent the ligand colliding with the atoms around the the pocket. So I have to define a box whose long axis is parallel to the pulling direction. Could anyone explain to me that how to define the box? Thanks in advance! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 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] genion doesn't recognize SOL in top file
Dear Gromacs users, I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -np 8 but it returns a error message saying: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' I checked the topol.top file, but SOL is indeed under [ molecules ] section: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 DRG 1 SOL 86574 I know it problem has been disscussed here before, but I cann't fix it out with the avialable information. Could you help me with it? Thanks in advance. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 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
答复: [gmx-users] topology file of ligand
Thank you Dr. Lemkul, Could you recommand some primary literatures which are most usefule for me to understand the force field? Yeping Sun Institute of Microbiology, Chinese Academy of Sciences --发件人：Justin Lemkul 发送时间：2013年10月16日(星期三) 00:05收件人：gromacs 主 题：Re: [gmx-users] topology file of ligandOn 10/15/13 11:24 AM, sunyeping wrote:> Dear gromacs users,>> I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he immediately notice three things that are wrong with this topology, which include charge group, H atom charge, etc.> And the author then reconstructed a topology file. I don't understand how the charge group and charge of individual atom are correctly assigned. Could you explain it to me?>The Gromos96 parameter sets assign charges and charge groups based on chemical functional groups that are transferable between molecules. Spotting inaccuracies and knowing how to fix them come with understanding how the force field was derived (read the primary literature and study existing molecules).-Justin-- ==Justin A. Lemkul, Ph.D.Postdoctoral FellowDepartment of Pharmaceutical SciencesSchool of PharmacyHealth Sciences Facility II, Room 601University of Maryland, Baltimore20 Penn St.Baltimore, MD 21201jalem...@outerbanks.umaryland.edu | (410) 706-7441==-- gmx-users mailing list gmx-users@gromacs.orghttp://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] topology file of ligand
Dear gromacs users, I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he immediately notice three things that are wrong with this topology, which include charge group, H atom charge, etc. And the author then reconstructed a topology file. I don't understand how the charge group and charge of individual atom are correctly assigned. Could you explain it to me? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 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
转发：[gmx-users] gromacs on GPU
Dear gromcas users, Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option "-testverlet" to mdrun in order to run it on GPU, it returns error "Fatal error:User non-bonded potentials are not (yet) supported with the Verlet schemeFor more information and tips for troubleshooting". Could you check the mdp file for me to see how to modefy it to make it suitable to GPU? Thanks in advance! integrator = mdnsteps = 5000dt = 0.002constraints = all-bondsnstcomm = 100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw =1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-Switch;Tcoupl = v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 4.5e-5ref_p = 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 500nstenergy = 100energygrps = chA chClincs-iter = 2DispCorr = EnerPresoptimize_fft = yes Yeping Sun -- 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] gromacs on GPU
Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option "-testverlet" to mdrun in order to run it on GPU, it returns error "nonbond potiential is not supported". Could you check the mdp file for me to see how to modefy it to make it suitable to GPU? Thanks in advance! integrator = mdnsteps = 5000dt = 0.002constraints = all-bondsnstcomm = 100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw =1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-SwitchTcoupl = v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 4.5e-5ref_p = 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 1nstenergy = 5000energygrps = chA chClincs-iter = 2DispCorr = EnerPresoptimize_fft = yes Yeping Sun -- 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] GROMACS on GPU
Dear gromacs users, Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option "-testverlet" to mdrun in order to run it on GPU, it returns error "nonbond potiential is not supported". Could you check the mdp file for me to see how to modefy it to make it suitable to GPU? Thanks in advance! Yeping Sun -- 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
