Re: [gmx-users] NPT simulation stage
Hi Lemkul, I am trying to simulate guanidium in water. My system contains 198 guanidium residues. But when I'm trying to use the grompp command ,I'm facing the problem of fudgeQQ, qi ,qj. I don't know what that means. I don't know how to rectify the error too. Plus if there are too many solvet molecules, how do I delete it ? Thanks, Swetha From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Sunday, April 27, 2014 9:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] NPT simulation stage On 4/27/14, 6:03 AM, Mahboobeh Eslami wrote: dear justin Thank you for your reply. My system is about 123,000 atoms and my box is cubic. I'm following conditions apply: pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 refcoord_scaling = com But the average pressure is not good repeatability. To fix this problem I did two NPT simulation stage The first 100ps by brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not good repeatability. I frequently change tau_p but I did not get any results. Increase the NPT simulation time did not solve the problem. I strongly need your help Thank you sincerely for your kindness What I was asking for previously were the actual results - i.e. what values of pressure you achieved. Please provide the exact g_energy output. When you increased the time, how long were the new runs? 100 ps is fairly short for any NPT process. Some systems may take a few ns to converge, depending on what their contents are. -Justin On Friday, April 25, 2014 5:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote: hi GMX users please help me i want to simulate protein-ligand complex by gromacs4.6.5 when i repeat NPT simulation stage many times, simulation results are very different for the pressure average.I sincerely thank you for your guidance Pressure is probably the most ill-defined quantity in MD simulations. It can fluctuate dramatically. Without the actual numbers, it's hard to comment, but issues related to pressure have been discussed extensively over the list in the past and there is useful information in http://www.gromacs.org/Documentation/Terminology/Pressure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] guanidinium in water
Hi Lemkul, genbox -cp test.gro -cs spc216.gro -box 24 24 24 -o watGND.gro Actually I want to do a simulation for 7M concentration. So, since the conc of 3M is already done, I did a small calculation of mass of 3M/avogadro number = 7M* Mixed mass(Mgnd+Mcl/ratio)*V .From this,I got the volume.From this, the box size was 24 24 24 . Thus I used this in the genbox. Output configuration contains 1384837 atoms in 461568 residues Volume : 13824 (nm^3) Density: 998.941 (g/l) Number of SOL molecules: 461549 Next,grompp command grompp -f ions.mdp -c watGND.gro -p system.top -o ions.tpr My system.top file #include gromos43a1.ff/forcefield.itp #include spc.itp #include gnd.itp [ molecule ] ; Name guanidium in water [ molecule ] ; Compound#molecule GND 19 SOL 461549 CL-38 ~ My ions.mdp file ions.mdp - used as input into grompp to generate ions.tpr ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 0 ; For exact run continuation or redoing part of a run init_step= 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 10 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 grompp -f ions.mdp -c watGND.gro -p system.top -o ions.tpr Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This is the trouble Im facing. Hoping for a positive reply soon. Regards, Swetha From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Sunday, April 27, 2014 11:38 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] guanidinium in water Please don't hijack an unrelated thread with a new question. I am re-titling this message; in the future, just send a new email when you have a new question. On 4/27/14, 11:11 AM, Swetha Srinivasan wrote: Hi Lemkul, I am trying to simulate guanidium in water. My system contains 198 guanidium residues. But when I'm trying to use the grompp command ,I'm facing the problem of fudgeQQ, qi ,qj. I don't know what that means. I don't know how to rectify the error too. Plus if there are too many solvet molecules, how do I delete it ? FudgeQQ is explained in the manual. Beyond that, you need to provide more details. What is in your topology? Did you create it yourself, or did you get it from some other source? What is the *exact* error message from grompp (copied and pasted from the terminal)? As for solvent removal, you'll have to tell us how you added solvent in the first place. Presumably this was done with genbox, in which case you can use -maxsol, but that's often not a good idea because it will leave voids in the simulation box. If the box is too large, you'll have to set up an appropriate one with editconf (or possibly genbox, but I'm still guessing here because you haven't provided any of your commands). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi Lemkul, If you tell me the exact steps I need to follow,I would be able to execute it. Please help me out with this. Thanks, Swetha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi lemkul, How do I correct the topology file? And which file is it? Thanks, Swetha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] guanidinium in water
Hi Lemkul, How do I correct this.Could you please help me? Thanks, Swetha From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Sunday, April 27, 2014 12:25 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] guanidinium in water On 4/27/14, 12:20 PM, Swetha Srinivasan wrote: Hi Lemkul, I had already used a rhein-water system before. I just edited that and gave my inputs. I don't really know what that means, but the bottom line is you have an incorrectly formatted line in the topology. It's under [pairs], it's function type 2, and it doesn't specify parameters correctly. See manual section 5.3.4. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi, My mail id is ssrin...@syr.edu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Hi, I don't know how to post my queries.Could you help me with that. Thanks, Swetha From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Swetha Srinivasan ssrin...@syr.edu Sent: Saturday, April 26, 2014 10:14 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] (no subject) Hi, My mail id is ssrin...@syr.edu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
