Re: [gmx-users] Placing system at the centre of the box.
Hi Rajan, The center of the system is the center of mass, not the center of the bounding box. Cheers, Tsjerk On Sat, Mar 14, 2015 at 8:41 PM, Rajan Kumar kumarrajan...@gmail.com wrote: Hi Tsjerk, Please see the box here https://www.dropbox.com/s/cu70fw2dmwaxl1x/Editconf.png?dl=0. On Sat, Mar 14, 2015 at 1:38 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Rajan, Do you see the box? From your output it is easily seen that the new center equals 0.5*boxvectors. Cheers, Tsjerk On Mar 14, 2015 5:47 AM, Rajan Kumar kumarrajan...@gmail.com wrote: Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of epoxide group on one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. I used the following commands to generate .gro. editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 -c - Read 260 atoms No velocities found system size : 1.845 1.562 1.523 (nm) center : 0.985 0.828 0.380 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 0.515 0.672 1.120 (nm) new center : 1.500 1.500 1.500 (nm) new box vectors : 3.000 3.000 3.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 27.00 (nm^3) My question is, what is this* center* and how is it calculated by editconf? When I see conf.gro in VMD, I don't actually see my system at the geometric center of the box. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] About gromacs/orca question.
原始邮件 主题: About gromacs/orca question. 日期: 14.03.2015 02:36 发件人: xzhao11 xzha...@uci.edu 收件人: christoph.riplin...@gmail.com Hi,gromacs users As a beginner of gromacs/orca for qm/mm, I have some questions to ask you. In fact，the resources about gromacs/orca are rare; my questions are: If I run a QM/MM Surface Scans, how to define key words? Such as ,bOPT and bTS , or need other key words in the mdp file? In a Microiterative optimization ( or ORCA QM/MM Optimization), how to produce MM regions point charges files and Lennard Jones coefficients file; in fact, I read the ORCA manual ,I only know the format of point charges files, but I want to know further details. Are the two files produced from previous step Conventional QM/MM Minimization? If possible, Can you provide some key examples of qm/mm input files, especially ORCAINFO file and its mdp file. Thank you for your help！ Best wishes！ xi -- 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] Placing system at the centre of the box.
Hi Tsjerk, Please see the box here https://www.dropbox.com/s/cu70fw2dmwaxl1x/Editconf.png?dl=0. On Sat, Mar 14, 2015 at 1:38 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Rajan, Do you see the box? From your output it is easily seen that the new center equals 0.5*boxvectors. Cheers, Tsjerk On Mar 14, 2015 5:47 AM, Rajan Kumar kumarrajan...@gmail.com wrote: Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of epoxide group on one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. I used the following commands to generate .gro. editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 -c - Read 260 atoms No velocities found system size : 1.845 1.562 1.523 (nm) center : 0.985 0.828 0.380 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 0.515 0.672 1.120 (nm) new center : 1.500 1.500 1.500 (nm) new box vectors : 3.000 3.000 3.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 27.00 (nm^3) My question is, what is this* center* and how is it calculated by editconf? When I see conf.gro in VMD, I don't actually see my system at the geometric center of the box. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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] Jump in potential after extension
Hi, I extend my simulation with same node on same machine, but when I check g_energy I find a gap in potential, why is that so?. (for example if before the extension the average value of potential were X, just as soon as extension starts the average jumps to Y.) my run command: aprun -n 1 tpbconv_mpi -s production.tpr -extend 10 -o production.tpr aprun-n 224 mdrun_mpi -s production.tpr -cpi state.cpt -c production.gro thank you in advance, Best regards -- 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] Placing system at the centre of the box.
Hi Rajan, Do you see the box? From your output it is easily seen that the new center equals 0.5*boxvectors. Cheers, Tsjerk On Mar 14, 2015 5:47 AM, Rajan Kumar kumarrajan...@gmail.com wrote: Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of epoxide group on one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. I used the following commands to generate .gro. editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 -c - Read 260 atoms No velocities found system size : 1.845 1.562 1.523 (nm) center : 0.985 0.828 0.380 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 0.515 0.672 1.120 (nm) new center : 1.500 1.500 1.500 (nm) new box vectors : 3.000 3.000 3.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 27.00 (nm^3) My question is, what is this* center* and how is it calculated by editconf? When I see conf.gro in VMD, I don't actually see my system at the geometric center of the box. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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] Query: Protein-ligand simulation
Dear all, For a protein-ligand simulation, how to confer to the system regarding hydrogen bonds. For example if the hydrogen bond is between ligand - N-H and Glu 282 , what command should be used? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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] Query: Protein-ligand simulation
On 3/14/15 11:17 AM, Priya Das wrote: Dear all, For a protein-ligand simulation, how to confer to the system regarding hydrogen bonds. For example if the hydrogen bond is between ligand - N-H and Glu 282 , what command should be used? gmx hbond with suitable index groups. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
