Re: [gmx-users] (no subject)
On 9/30/13 5:19 AM, suhani nagpal wrote: Greetings I have a large protein of 303 residues and one of the lysine is acetylated in the same. The forcefield selection according to the options says as follows: Residue 'ALY' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors How to work and get a gro file for the pdb. http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Justin -- == 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
Re: [gmx-users] (no subject)
On 9/14/13 7:31 AM, mabbasi wrote: Dear All users I used OPLS ff for my system. After md production I get this error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- == 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
Re: [gmx-users] (no subject)
On 9/3/13 7:20 AM, Prajisha Sujaya wrote: Respected sir, I am facing a problem while simulating the tRNA molecule while converting pdb to gro, Fatal error: Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms while sorting atoms. force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P. kindly give valuable suggestion how to rectify this error, http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry -Justin -- == 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
Re: [gmx-users] (no subject)
On 6/20/13 11:11 PM, Hari Pandey wrote: Hi all gromacs users I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. What I want is: after some ps, temperature of A and C should be constant (i.e reach up to steady state) and B may not be. for that My NVT.mdp is: ; simulation at 300K and 2 ps is on constraints =all-bonds integrator =md dt =0.001 ; ps nsteps =10 ; total 100 ps nstcomm =10 nstxout =1000 nstxtcout =0 nstvout =0 nstfout =0 nstenergy =100 nstlist =100 ns_type =grid rlist =0.5 coulombtype =pme rcoulomb=0.5 vdwtype =cut-off rvdw=0.5 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes DispCorr=no ;Brendsen tempereture coupling is on Tcoupl = nose-hoover tau_t =0.001 -1 0.001 tc-grps =A B C ref_t =750 300 350 ;pressure coupling is on Pcoupl =no Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =yes gen_temp=750 300 350 gen_seed=-1 MY NPT.mdp is: ( here all output control parameters also) ;Brendsen tempereture coupling is on Tcoupl =nose-hoover tau_t =1 -1 1 tc-grps =NCALPHA MIDDLE NCNN ref_t =750 300 350 ;pressure coupling is on Pcoupl =Berendsen Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =1 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no gen_temp=750 300 350 gen_seed=-1 MY NVE.mdp is: ( here all output control parameters also) tc-grps = A B C ref_t =750 300 300 energygrps = NCALPHA MIDDLE NCNN tcoupl = nose-hoover tau-t = 1 -1 1 ;pressure coupling is on Pcoupl =no ;Pcoupltype =isotropic ;tau_p =0.5 ;compressibility =1e-5 ;ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no ; gen_temp=750 300 350 ; gen_seed=-1 What I did is: pdb2gmx - argnew.pdb -o fws.pdb -p fws.top; editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0; grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5; mdrun -deffnm em -v; grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx -o nvt.tpr -maxwarn 5; mdrun -deffnm nvt -v; grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx -o npt.tpr -maxwarn 5; mdrun -deffnm npt -v grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx -o nve.tpr -maxwarn 5; mdrun -deffnm nve -v; g_energy -f nve.edr -s nve.tpr -o F1.xvg But the system do not get equilibrated and A, B has not steady state temperature after time even 100 ps. please help me, where I did wrong See my previous reply: http://lists.gromacs.org/pipermail/gmx-users/2013-June/082392.html -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] (no subject)
I really don't think thats possible at the moment. All interactions in Reax, if I recall correctly, are dependent on bond order, which is not an implemented concept in gromacs. Erik On 6 May 2013, at 12:51, Sathish Kumar sathishk...@gmail.com wrote: hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein -- regards M.SathishKumar -- 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] (no subject)
On 5/5/13 5:10 AM, Group Gro wrote: Dear GROMACS users, I am working on protein-ligand complexes and when I run mdrun -deffnm nvt.tpr -v I run into this error: Fatal error: 2 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. I found the best docked position of my ligand by Autodock run and copied the best position of my ligand in a pdb format. Then I ran PRODRG to provide gro and itp files. I have tried different drugs as ligand and all of them are OK. I searched the mailing list and found other users have had this error. I understood that my system would be unstable. What should I do to solve this problem? Start with a better topology. PRODRG topologies produce bad results. http://pubs.acs.org/doi/abs/10.1021/ci100335w -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] (no subject)
On Wed, Apr 10, 2013 at 3:49 PM, Liron Cohen liron.co...@weizmann.ac.ilwrote: hi, i am using gromacs 4.5 and i am trying to run an energy minimization and then temperature equilibration for a system of two charged plates plates solvented in water. the plates are made of fake atoms which has carbon atoms parameters, and a bond length of 0.2 nm. the plates are made from o configuration of 6x6 of these atoms. each located in a distance of 0.2 nm from the other. energy minimization is working just fine, but as i try to run the temperature equilibration i get the following warning: Warning: 1-4 interaction between 49 and 67 at distance 6.967 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation and also a bunch of these warnings: t = 0.019 ps: Water molecule starting at atom 8260 can not be settled. the EM file is: title = Test_mg_water cpp = /usr/bin/cpp -traditional; the c pre-processor define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 10 nstxout = 100 nstlist = 1 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 optimize_fft = yes pme_order = 4 ewald_rtol = 1e-5 ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 ; freeze the solute and ions freezegrps = GAP GAN freezedim = Y Y Y Y Y Y energygrps = GAP GAN *** (GAP and GAN are the charged plates) the temperature equilibration file is: title = Heat@constant volume cpp = /usr/bin/cpp -traditional; the c pre-processor ; define = -DPOSRES ; constraints = none nstlist = 1 pbc = xyz rlist= 1.0 ;domain-decomposition = yes coulombtype = PME-switch rcoulomb = 0.9 epsilon-r= 1 vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 DispCorr = EnerPres epsilon_surface = 0 integrator = sd tinit= 0 dt = 0.002 nsteps = 37500 ; 75 psec nstcomm = 1000 nstfout = 0 ;kys nstlog = 1000 nstenergy= 100 nstxtcout= 100 nstxout = 100 nstvout = 5 xtc_precision= 1000 xtc_grps = SYSTEM ns_type = grid tc_grps = SYSTEM tau_t= 0.1 ref_t= 300 ;tcoupl = nose-hoover ;constraints = hbonds constraint-algorithm = Lincs ;unconstrained-start = no shake-tol= 0.0001 lincs-order = 4 lincs-warnangle = 30 lincs_iter= 2 ;freezegrps = SFP SFN ;freezedim = Y Y Y Y Y Y fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Type of annealing for each temperature group (no/single/periodic) annealing= single ; Number of time points to use for specifying annealing in each group annealing_npoints= 4 ; List of times at the annealing points for each group annealing_time = 0 25 50 75 ; Temp. at each annealing point, for each group. annealing_temp = 5 150 300 300 gen_seed = 6594 gen_temp = 5 the initial coordinates of the plates are: Good ROcking Metal Altar for Chronical Sinners 72 1GAP G11 1.750 2.000 1.750 1GAP G22 1.750 2.000 1.950 1GAP G33 1.750 2.000 2.150 1GAP G44 1.750 2.000 2.350 1GAP G55 1.750 2.000 2.550 1GAP G66 1.750 2.000 2.750 1GAP G77 1.950 2.000 1.750 1GAP G88 1.950 2.000 1.950 1GAP G99 1.950 2.000 2.150 1GAPG10 10 1.950 2.000 2.350 1GAPG11 11 1.950 2.000 2.550 1GAPG12 12 1.950 2.000 2.750 1GAPG13 13 2.150 2.000 1.750 1GAPG14 14 2.150 2.000 1.950 1GAPG15 15 2.150 2.000 2.150 1GAPG16 16 2.150 2.000 2.350 1GAPG17 17 2.150 2.000 2.550 1GAPG18 18 2.150 2.000 2.750 1GAPG19 19 2.350 2.000 1.750 1GAPG20 20 2.350 2.000 1.950 1GAPG21 21 2.350 2.000 2.150 1GAPG22 22 2.350 2.000 2.350 1GAPG23 23 2.350 2.000 2.550 1GAPG24 24 2.350 2.000 2.750 1GAPG25 25 2.550 2.000 1.750 1GAPG26 26 2.550 2.000 1.950 1GAPG27 27 2.550 2.000 2.150 1GAPG28 28 2.550 2.000 2.350 1GAPG29 29 2.550 2.000 2.550 1GAPG30 30 2.550 2.000 2.750 1GAPG31 31 2.750 2.000 1.750
RE: [gmx-users] (no subject)
Hi Jeremy, I am not an expert of amber ff, but what I have notice form the ffbonded.itp file of amber99sb is that it does not have an improper header and it might use dihedraltypes for both proper and improper; or constratinttypes. It would be good to get a comment from someone who knows how amber works well. Another problem might be with your atom names ( CAD OAX CAB CAG ) . If the atom names of your ligand are not available in the amber99sb ff, when you generate your top/itp file it wont understand them. If you want include new atom/molecule it is always good to get the parameters from some other literature or use the very similar kind of atoms to generate an itp and check whether your parameters are good or bad by calculating some other physicochemical property. By the way, you can include your atom/molecules or new parameters in general in amber99sb or any force field and generate you're an itp file for your new molecules. But you have to be careful not to mess up other parts of the ff. Or you can create your own copy and incorporate in the simulation package (top folder). It would be good if you explain what you are trying to do in detail to get more productive help. Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yongliang Yang Sent: Monday, 25 March 2013 5:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] (no subject) Dear EB, Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, No default proper dih. types'. Any advice? Thanks! Cheers Jeremy --- Hi Jeremy, I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section Yours look like [ impropers ] CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and force constant) Whereas the program is looking for CT CT OS CT9 0.0 1.60247 3 (here function, angel, force constant and multiplicity??) copied from the amber bonded force field parameter :) I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation. Cheers, EB -- 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] (no subject)
On 3/25/13 2:37 AM, Emanuel Birru wrote: Hi Jeremy, I am not an expert of amber ff, but what I have notice form the ffbonded.itp file of amber99sb is that it does not have an improper header and it might use dihedraltypes for both proper and improper; or constratinttypes. It would be good to get a comment from someone who knows how amber works well. The directive is [dihedraltypes]. One can differentiate between propers and impropers by looking at the function type (see Table 5.5 in the manual). Another problem might be with your atom names ( CAD OAX CAB CAG ) . If the atom names of your ligand are not available in the amber99sb ff, when you generate your top/itp file it wont understand them. If you want include new atom/molecule it is always good to get the parameters from some other literature or use the very similar kind of atoms to generate an itp and check whether your parameters are good or bad by calculating some other physicochemical property. Atom names are not what ffbonded.itp uses. Interaction types are defined by atom types. -Justin By the way, you can include your atom/molecules or new parameters in general in amber99sb or any force field and generate you're an itp file for your new molecules. But you have to be careful not to mess up other parts of the ff. Or you can create your own copy and incorporate in the simulation package (top folder). It would be good if you explain what you are trying to do in detail to get more productive help. Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yongliang Yang Sent: Monday, 25 March 2013 5:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] (no subject) Dear EB, Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, No default proper dih. types'. Any advice? Thanks! Cheers Jeremy --- Hi Jeremy, I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section Yours look like [ impropers ] CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and force constant) Whereas the program is looking for CT CT OS CT9 0.0 1.60247 3 (here function, angel, force constant and multiplicity??) copied from the amber bonded force field parameter :) I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation. Cheers, EB -- 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] (no subject)
Thanks Justin, sorry for using the wrong word what I had to mention was atom type not name. Jeremy, as per Justin's comment I guess you better work out what kind of parameters you have to use for your impropers. The functions that you should put in you ligand itp file should be the same as amber ff. Cheers, On 25/03/2013, at 9:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/25/13 2:37 AM, Emanuel Birru wrote: Hi Jeremy, I am not an expert of amber ff, but what I have notice form the ffbonded.itp file of amber99sb is that it does not have an improper header and it might use dihedraltypes for both proper and improper; or constratinttypes. It would be good to get a comment from someone who knows how amber works well. The directive is [dihedraltypes]. One can differentiate between propers and impropers by looking at the function type (see Table 5.5 in the manual). Another problem might be with your atom names ( CAD OAX CAB CAG ) . If the atom names of your ligand are not available in the amber99sb ff, when you generate your top/itp file it wont understand them. If you want include new atom/molecule it is always good to get the parameters from some other literature or use the very similar kind of atoms to generate an itp and check whether your parameters are good or bad by calculating some other physicochemical property. Atom names are not what ffbonded.itp uses. Interaction types are defined by atom types. -Justin By the way, you can include your atom/molecules or new parameters in general in amber99sb or any force field and generate you're an itp file for your new molecules. But you have to be careful not to mess up other parts of the ff. Or you can create your own copy and incorporate in the simulation package (top folder). It would be good if you explain what you are trying to do in detail to get more productive help. Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yongliang Yang Sent: Monday, 25 March 2013 5:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] (no subject) Dear EB, Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, No default proper dih. types'. Any advice? Thanks! Cheers Jeremy --- Hi Jeremy, I have checked how improper dihedral should look like in Amber, guessing that you used amber99sb force field. But I am wondering from where the improper in your ligand.itp was generated. As it doesn not look alike with the amber force field. It actually is not the problem of multiplicity but the number of parameters that you put in the improper is not enough. It should be at least three parameters in the improper section Yours look like [ impropers ] CAD OAX CAB CAG 0.000 167.4 (two parameters here angle and force constant) Whereas the program is looking for CT CT OS CT9 0.0 1.60247 3 (here function, angel, force constant and multiplicity??) copied from the amber bonded force field parameter :) I think you should generate a logical itp file which fullfil all the necessary requirements before you run you simulation. Cheers, EB -- 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 -- 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] (no subject)
On 1/9/13 8:57 AM, sara azhari wrote: Dear Justin first ,I get error on atom number . after change emtol to 10 , I get same error on atom number . what' your idea? how to solve it? mdrun probably did a different number of steps and/or moved through configurations different. The bottom line is there is something wrong with whatever coordinates you are providing it such that the minimization cannot be successfully finished. I use this file for PR step , but I get this error: Proceeding when a simple energy minimization has failed is futile. Your system is far too unstable for a simulation. -Justin A charge group moved too far between two domain decomposition your system might be not equilibrated well enough my system without charge (total charge is zero) what' your idea? thanks -- 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] (no subject)
On 1/6/13 7:29 AM, fatemeh ramezani wrote: I didn't set epsilon and sigma between au and other atoms equal to zero, but I have not enteredanyEpsilon and Sigmafor them , and once again I set them zero and try it again. If you didn't set them at all, grompp should have given a fatal error. But if closing of gold to protein, is because of charge, how do I delete its effect ? How can I uncharged the system? (Of course, the whole system charge that is shown in the first grompp step is very low near -0.11). If your system has a net charge of -0.11, the topology is incorrect. Fractional charges on the system are nonphysical. -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] (no subject)
On 12/17/12 12:53 PM, Shine A wrote: sir, I am studying dynamics of a membrane protein using oplsaa force field. Energy minimization during nvt equilibration getting error like this. 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. plz give me a way to solve this problem? http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group -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
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On 10/3/12 5:17 PM, Ho, Tuan A. wrote: Dear Gromacs users, I would like to simulate water on Ruthenium surface. Would you please suggest the force field used to describe Ru. You're not likely to find one built into Gromacs by default. http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -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
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On 8/28/12 1:25 PM, Lingyun Wang wrote: Hi all, I want to model a protein on the surface of a bilayer membrane. Is it reasonable to add less water molecules to the bilayer side without protein? Or the water should be the same on both side of membrane? Thanks. Given periodic boundaries conditions, the amount of water on either side is irrelevant. -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] (no subject)
On 8/2/12 10:09 AM, vidhya sankar wrote: Dear Gromacs user , I Write Some linux .sh programming to automate grompp and mdrun process in Clustering which is as Follows Could Any one of you point out the error in following script files ? is it correct or not. Are you getting an error message? If so, what is it? Why are you using -maxwarn with grompp? There's rarely a good reason to do so. There's also no reason to redefine environment variables if their values are not changed, so you can save yourself a few lines. -Justin #!/bin/bash #! -l nodes=1:ppn=4 # load the modules # preproc source=/usr/local/plumedmpigromacs/bin GROMPP=/usr/local/plumedmpigromacs/bin/grompp_mpi_d MDRUN=/usr/local/plumedmpigromacs/bin/mdrun_mpi_d $GROMPP -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index0.ndx -o 232npt0.tpr -maxwarn 1 -po mdout0.mdp /dev/null mpirun -np 4 $MDRUN -deffnm 232npt0 -cpi 232npt0_prev.cpt /dev/null #exit # preproc source=/usr/local/plumedmpigromacs/bin GROMPP=/usr/local/plumedmpigromacs/bin/grompp_mpi_d MDRUN=/usr/local/plumedmpigromacs/bin/mdrun_mpi_d $GROMPP -f npt_umbrella.mdp -c conf153.gro -p topol.top -n index153.ndx -o 232npt153.tpr -maxwarn 1 -po mdout153.mdp /dev/null mpirun -np 4 $MDRUN -deffnm 232npt153 /dev/null #exit Thanks in Advance With Regards S. Vidhya sankar -- 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
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On 7/14/12 3:34 AM, sara elham wrote: Dear Gromacs users I want to find the solution for my problem from mailing list, but it give me this massage: Timeout expired. The timeout period elapsed prior to completion of the operation or the server is not responding. The website experiences intermittent issues. Hopefully they will be sorted out soon. I tried to registration again, but in the section Type the characters you see in the image below , it isn't shown anything!!! You don't need to register to search the mailing list archive. -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
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On 7/11/12 6:00 AM, amir abbasi wrote: Hi All! I want to use Implicit solvent to simulate a nucleic acid sequence. How can I do it? I use this command: genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname CL -neutral -conc 0.1 ions.tpr file is same as umbrella sampling tutorial. I got this error message: Fatal error: Your solvent group size (2898) is not a multiple of 31 what should I do? One does not typically add explicit ions in an implicit solvent system. genion fails because it appears you are trying to replace parts of your nucleic acid with ions. -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
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Thanks Justin, But I want to neutralize my system in implicit solvent. In Amber I had use Debye screening but in gromacs I don't know what should I do. On Wed, Jul 11, 2012 at 2:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/11/12 6:00 AM, amir abbasi wrote: Hi All! I want to use Implicit solvent to simulate a nucleic acid sequence. How can I do it? I use this command: genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname CL -neutral -conc 0.1 ions.tpr file is same as umbrella sampling tutorial. I got this error message: Fatal error: Your solvent group size (2898) is not a multiple of 31 what should I do? One does not typically add explicit ions in an implicit solvent system. genion fails because it appears you are trying to replace parts of your nucleic acid with ions. -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] (no subject)
On 7/11/12 6:19 AM, amir abbasi wrote: Thanks Justin, But I want to neutralize my system in implicit solvent. In Amber I had use Debye screening but in gromacs I don't know what should I do. From my understanding, this remains an unresolved issue. -Justin On Wed, Jul 11, 2012 at 2:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/11/12 6:00 AM, amir abbasi wrote: Hi All! I want to use Implicit solvent to simulate a nucleic acid sequence. How can I do it? I use this command: genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname CL -neutral -conc 0.1 ions.tpr file is same as umbrella sampling tutorial. I got this error message: Fatal error: Your solvent group size (2898) is not a multiple of 31 what should I do? One does not typically add explicit ions in an implicit solvent system. genion fails because it appears you are trying to replace parts of your nucleic acid with ions. -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
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On 6/19/12 8:58 AM, ankita oindrila wrote: I am doing simulation of membrane protein in lipid bilayer for my college project!. After making the complex of protein and lipid bilayer, I was going to the step using genbox to solvate the system. The error that i am now getting is : Fatal error: Not enough memory. Failed to realloc 1008588696 bytes for nlist-jjnr, nlist-jjnr=0x20026008 (called from file ns.c, line 537) what should i do?? If you need nearly 1 GB to solvate a system, it must be incredibly large. Consult the following: http://www.gromacs.org/Documentation/Errors#Cannot_allocate_memory -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] (no subject)
On 6/18/12 4:55 AM, ankita oindrila wrote: i am doing protein in bilipid membrane simulation. while packing the protein in the lipid membrane step, i am getting this error. command : perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 300. This error usually comes up when there is something wrong with the format of the input .gro file. -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
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On 6/13/12 5:09 AM, Seera Suryanarayana wrote: Dear all gromacs users, I am doing moleculer dynamics by using gromacs software.I got the following error after using the commond mdrun -deffnm nvt. Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated. Kindly tell me how to overcome this error. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -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
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On 12/06/2012 3:18 PM, tarak karmakar wrote: Dear All , I am facing problem in matching the coordinates number in this two files, em.gro and toplogy.top. I have tried with changing the number of solvents, adding ions (Na+) but in vain _Note :: My system has ' -1.00 ' charge ...so I have added one Sodium ion_ So can anyone please get me out of this trouble ??? Fatal error: number of coordinates in coordinate file (em.gro, 64506) does not match topology (toplogy.top, 64504) Probably you didn't use genion properly, but unless you show us your command lines and [molecule] section, we can't help. Mark -- /*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 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] (no subject)
Could you paste your .top file and the command your add ions? Maybe the Cl- ion was also added when you added Na+ ion? On Tue, Jun 12, 2012 at 1:18 PM, tarak karmakar tarak20...@gmail.comwrote: Dear All , I am facing problem in matching the coordinates number in this two files, em.gro and toplogy.top. I have tried with changing the number of solvents, adding ions (Na+) but in vain *Note :: My system has ' -1.00 ' charge ...so I have added one Sodium ion* So can anyone please get me out of this trouble ??? Fatal error: number of coordinates in coordinate file (em.gro, 64506) does not match topology (toplogy.top, 64504) -- *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 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
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On 31/05/2012 9:37 PM, Subramaniam Boopathi wrote: how to assign charge and charge group number when new residue as being added to the existing amino acid rtp file Read about the file format in the manual. 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
Re: [gmx-users] (no subject)
On 5/31/12 7:37 AM, Subramaniam Boopathi wrote: how to assign charge and charge group number when new residue as being added to the existing amino acid rtp file The details depend on the force field you're using. http://www.gromacs.org/Documentation/How-tos/Parameterization -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
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On 5/16/12 8:49 AM, rama david wrote: Hi Gromacs Friends, I plan to simulate protein In Trifluoro Ethanol solvent using G96 53a6 FF Please help to define parameters in md.mdp For water I am using following mdp file lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 0.9; short-range neighborlist cutoff (in nm) rcoulomb= 0.9; short-range electrostatic cutoff (in nm) vdw-type= Cut-off rvdw= 1.4; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME For TFE and water mix of different conc , What should be the mdp file parameter ??? I am using following ones.. Twin range cutt-off for nnonbonded interactions.. Short range cut-off 0.8 and long range 1.4 for both coulombic and lennard-jones Short range updates for every 5 step togather with pair list.. Please give me valuable suggestion .. The settings given in an .mdp file are dependent upon the force field, not the molecules in the system. So if you have water or water/TFE, the requirements of the force field are still the same. -Justin -- Justin A. Lemkul, Ph.D. 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
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Anik Sen wrote: Respected Sir, I am new to gromacs. Am using GROMACS 4.5.5 version. I have two questions.. 1. I want to know about plotting the co-ordination number (CN) of the water molecules around one of my substrate say a KCl molecule for example. What should i do to get the CN number. There are extensive discussions on this topic in the list archive, including possible use of RDF or other software. I'd suggest you search for this information. 2. I have three different substrates. I want to create a same box size irrespective of the size of my molecule and generate same number of water molecules around them. What should I do? I doubt you can have both. For a given box size, if the solute molecule occupies a different volume, then less water molecules will fit in the box. If you limit the number of water molecules around your smallest solvent in the given box, you will have voids within the box that will either collapse under NPT (leading to the box size decreasing) or will cause the formation of small vacuum pockets under NVT (which is not realistic in the condensed phase, obviously). You can obtain either using editconf -box (to define a particular box size) or genbox -maxsol (to set a maximum value of solvent). Whether or not you can accomplish what you want in a sound manner (or whether it is even necessary) is debatable. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
saly jackson wrote: Hi, I want to add 8 of a molecule including 6 atoms. But when I run each of the following commands I System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1948, nrj = 22927 Try 63309box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 3 Coulomb: 3 LJ: 3 System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1946, nrj = 22921 Try 63310box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 3 Coulomb: 3 LJ: 3 System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1930, nrj = 22871 Try 63311box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 3 Coulomb: 3 LJ: 3 System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1930, nrj = 22911 Try 63312box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 3 Coulomb: 3 LJ: 3 System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1930, nrj = 22885 Try 63313box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 3 Coulomb: 3 LJ: 3 System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1935, nrj = 22846 Try 63314box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 3 Coulomb: 3 LJ: 3 System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1936, nrj = 22827 Try 63315box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 3 Coulomb: 3 LJ: 3 System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1930, nrj = 22863 Try 63316box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 3 Coulomb: 3 LJ: 3 System total charge: 0.000 Killed You haven't shown your actual comment, but I assume it's some form of genbox -ci -nmol. This is a rather impractical approach to adding such a large amount of molecules, as your system's memory may get exhausted, which I suspect is the case here. The better approach is to use genconf -nbox to generate a suitable grid of a smaller number of molecules, say a few hundred, then use genbox -cs -maxsol to fill a new box with the desired number of solvent molecules. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Hi You should compile your fftw with --enable-shared if you want to link your gromacs installation to shared libraries (which is the default in the latest versions). Check the installation instructions in the website. Javier El 11/01/12 08:20, Anik Sen escribió: Im having problems installing Gromacs. I followed the GROMACS installation instructions as suggested by justin. But in vain. The same error is coming again and again. Please suggest. The error file is given below: */usr/bin/ld: /usr/local/lib/libfftw3.a(plan-dft-r2c-3d.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC* */usr/local/lib/libfftw3.a: could not read symbols: Bad value* *collect2: ld returned 1 exit status* *make[3]: *** [libmd_d.la http://libmd_d.la/] Error 1* *make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src/mdlib'* *make[2]: *** [all-recursive] Error 1* *make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src'* *make[1]: *** [all] Error 2* *make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src'* *make: *** [all-recursive] Error 1* Thanx in advance Anik Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 www.csmcri.org -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Phone: (+34)868887434 -- 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] (no subject)
I have already done that but the problem persisits. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Javier Cerezo [j...@um.es] Sent: Wednesday, January 11, 2012 1:56 PM To: gmx-users@gromacs.org Subject: Re: [gmx-users] (no subject) Hi You should compile your fftw with --enable-shared if you want to link your gromacs installation to shared libraries (which is the default in the latest versions). Check the installation instructions in the website. Javier El 11/01/12 08:20, Anik Sen escribió: Im having problems installing Gromacs. I followed the GROMACS installation instructions as suggested by justin. But in vain. The same error is coming again and again. Please suggest. The error file is given below: /usr/bin/ld: /usr/local/lib/libfftw3.a(plan-dft-r2c-3d.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd_d.lahttp://libmd_d.la/] Error 1 make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 Thanx in advance Anik Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Phone: (+34)868887434 -- 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] (no subject)
On 11/01/2012 10:07 PM, Anik Sen wrote: I have already done that but the problem persisits. Get a clean tarball of FFTW3 and follow http://www.gromacs.org/Downloads/Installation_Instructions#Details_for_building_the_FFTW_prerequisite. Probably you have a mess of previous configure commands, or didn't actually install the --enable-shared binaries. Mark *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Javier Cerezo [j...@um.es] *Sent:* Wednesday, January 11, 2012 1:56 PM *To:* gmx-users@gromacs.org *Subject:* Re: [gmx-users] (no subject) Hi You should compile your fftw with --enable-shared if you want to link your gromacs installation to shared libraries (which is the default in the latest versions). Check the installation instructions in the website. Javier El 11/01/12 08:20, Anik Sen escribió: Im having problems installing Gromacs. I followed the GROMACS installation instructions as suggested by justin. But in vain. The same error is coming again and again. Please suggest. The error file is given below: */usr/bin/ld: /usr/local/lib/libfftw3.a(plan-dft-r2c-3d.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC* */usr/local/lib/libfftw3.a: could not read symbols: Bad value* *collect2: ld returned 1 exit status* *make[3]: *** [libmd_d.la http://libmd_d.la/] Error 1* *make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src/mdlib'* *make[2]: *** [all-recursive] Error 1* *make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src'* *make[1]: *** [all] Error 2* *make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src'* *make: *** [all-recursive] Error 1* Thanx in advance Anik Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 www.csmcri.org -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Phone: (+34)868887434 -- 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] (no subject)
You need to post how did you exactly installed fftw and gromacs in order to get more help. It seems to me that the problem is related to the shared fftw libraries. Could you compile the gromacs binaries with --disable-shared? Javier El 11/01/12 12:07, Anik Sen escribió: I have already done that but the problem persisits. *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Javier Cerezo [j...@um.es] *Sent:* Wednesday, January 11, 2012 1:56 PM *To:* gmx-users@gromacs.org *Subject:* Re: [gmx-users] (no subject) Hi You should compile your fftw with --enable-shared if you want to link your gromacs installation to shared libraries (which is the default in the latest versions). Check the installation instructions in the website. Javier El 11/01/12 08:20, Anik Sen escribió: Im having problems installing Gromacs. I followed the GROMACS installation instructions as suggested by justin. But in vain. The same error is coming again and again. Please suggest. The error file is given below: */usr/bin/ld: /usr/local/lib/libfftw3.a(plan-dft-r2c-3d.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC* */usr/local/lib/libfftw3.a: could not read symbols: Bad value* *collect2: ld returned 1 exit status* *make[3]: *** [libmd_d.la http://libmd_d.la/] Error 1* *make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src/mdlib'* *make[2]: *** [all-recursive] Error 1* *make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src'* *make[1]: *** [all] Error 2* *make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/src'* *make: *** [all-recursive] Error 1* Thanx in advance Anik Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 www.csmcri.org -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Phone: (+34)868887434 -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Phone: (+34)868887434 -- 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] (no subject)
fftw-3.3 installation: first gone to the fftw3.3 folder ./configure --enable-threads --enable-float --enable-sse --enable-shared --prefix /home/ganguly/Gromacs/fftw3.3 . . . make . . . make install Then gromacs 4.5.5 is being installed. installation: first gone to the gromacs-4.5.5 folder ./configure --disable-shared [also done for ./configure --enable-shared] . . . make . . . make install same error is coming. The error is given below: After make command, the last few lines are this type:::-- make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html' Making all in images make[3]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images' Making all in online make[3]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online' make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html' make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' Making all in man make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' Making all in man1 make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1' Making all in man7 make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7' make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5' Then after the make install command :- [ganguly@localhost gromacs-4.5.5]$ make install Making install in include . . . . . /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/futil.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gbutil.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gen_ad.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/genborn.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_ana.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_arpack.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_blas.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_cyclecounter.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_fatal.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_fft.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_ga2la.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_lapack.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_matrix.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_parallel_3dfft.h': Permission denied make[3]: *** [install-pkgincludeHEADERS] Error 1 make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make: *** [install-recursive] Error 1 [ganguly@localhost gromacs-4.5.5]$ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Javier Cerezo [j...@um.es] Sent: Wednesday, January 11, 2012 5:12 PM To: gmx-users@gromacs.org Subject: Re: [gmx-users] (no subject) You need to post how did you exactly installed fftw and gromacs in order to get more help. It seems to me that the problem is related to the shared fftw libraries. Could you compile the gromacs binaries with --disable-shared? Javier El 11/01/12 12:07, Anik Sen escribió: I have already done that but the problem persisits. From: gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org
Re: [gmx-users] (no subject)
On 12/01/2012 5:44 PM, Anik Sen wrote: fftw-3.3 installation: first gone to the fftw3.3 folder ./configure --enable-threads --enable-float --enable-sse --enable-shared --prefix /home/ganguly/Gromacs/fftw3.3 . . . make . . . make install Then gromacs 4.5.5 is being installed. installation: first gone to the gromacs-4.5.5 folder ./configure --disable-shared [also done for ./configure --enable-shared] . . . make . . . make install same error is coming. The error is given below: After make command, the last few lines are this type:::-- make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html' Making all in images make[3]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/images' Making all in online make[3]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html/online' make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share/html' make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/share' Making all in man make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' Making all in man1 make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man1' Making all in man7 make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man/man7' make[2]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/man' make[1]: Entering directory `/home/ganguly/Gromacs/gromacs-4.5.5' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5' Then after the make install command :- [ganguly@localhost gromacs-4.5.5]$ make install Making install in include . . . . . /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/futil.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gbutil.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gen_ad.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/genborn.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_ana.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_arpack.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_blas.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_cyclecounter.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_fatal.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_fft.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_ga2la.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_lapack.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_matrix.h': Permission denied /usr/bin/install: cannot remove `/usr/local/gromacs/include/gromacs/gmx_parallel_3dfft.h': Permission denied make[3]: *** [install-pkgincludeHEADERS] Error 1 make[3]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ganguly/Gromacs/gromacs-4.5.5/include' make: *** [install-recursive] Error 1 [ganguly@localhost gromacs-4.5.5]$ I updated http://www.gromacs.org/Downloads/Installation_Instructions#Final_Installation to address this issue. 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
Re: [gmx-users] (no subject)
On 12/27/2011 5:38 PM, Nidhi Katyal wrote: Dear all, I am trying to create tmao box.Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I got a box where all water molecules got accumulated in two three small region within the box and tmao molecules in another small regions.I wanted near random uniform distribution of tmao in water. Perhaps the box didn't get equilibrated properly. Any help from user, where I am wrong and what should I do. Your SA protocol sounds like a recipe for problems. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation The usual process for generating a box of mixed solvents is here http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents but your cosolvent may be too large for the genbox -ci replacement procedure. Then, you may need to use the ideas here (http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation) to make a suitably dilute TMAO solution that can then be solvated with water with genbox -cs. Either way, lengthy equilibration will be in order. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] (no subject)
swati patel wrote: Hello, when executing this command g/_rompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr d ,fatal error is giving that Group reference not found in indexfile._/ Why am i getting this error?? You are calling a group named reference but no such group exists in the index file. You need to create the group and add it to the index file. Please also check the list archive when you get errors prior to posting. Almost every error produced by a Gromacs program you will encounter has been asked and answered. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
ibi2010...@iiita.ac.in wrote: Hello, I got all confused.So i started with the beginnning.i generated topology for my protein Streptavidin and generated topology for my ligand using prodrg2.5 server. I am getting error at step editconf i.e.Fatal error:Something is wrong in the coordinate formatting of file conf.gro. Any suggestions??I made necessary changes to topol.top and conf.gro to merge ligand topology. Something you did was wrong, but it's hard to say. The problem is with the coordinate file, so when you merged the protein and ligand, you broke the format somehow. There are many potential problems. Please work through the protein-ligand tutorial for a guide on how to properly deal with such systems. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Oh, thanks! On Thu, Oct 6, 2011 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Janani Ganesan wrote: Hi, Thanks for the reply! I tried the rates, and only the terminal with positive rate gets pulled. The first and the last amino acids are spatially oriented one behind the other. I think defining a vector might work better, but I am not sure why nothing happens when I define a pull_vec1 and pull_vec2. Am I missing anything? When setting distance as the pull_geometry, only pull_dim is used; pull_vec is ignored. If you want to define vectors, use the direction pull_geometry. -Justin Thanks, Sai On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Sai Janani Ganesan wrote: Hi, I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it. I define a different vector (pull_vec1 and pull_vec2) with +x and -x values and that does not even pull the protein I tried using only pull_group1 and pull_group2, without a reference, and neither groups get pulled. I chose different references, I do have some success but I don't think it is the best way to do it. How do I pull the N and C terminal apart, by simultaneously pulling them in opposite directions?Why is my vector definition wrong? This is my pull code: pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 2 pull_group0 = Chain-C pull_group1 = Chain-B pull_group2 = Chain-A %pull_vec1 = -31 0 0 %pull_vec2 = 31 0 0 I suspect the % signs will mess things up, but probably will give a fatal error, if nothing else. pull_rate1 = 0.002pull_k1 = 1000pull_rate2 = 0.002 pull_k2 = 1000 Here's the problem. You're telling the two pulled groups to move in the same direction. With distance geometry, the selections are a bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the groups will be pulled in opposite directions. Otherwise, you're just towing your protein along in the box. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- /Every sentence I utter must be understood not as an affirmation but as a question. - Niels Bohr/ -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**
Re: [gmx-users] (no subject)
Sai Janani Ganesan wrote: Hi, I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it. I define a different vector (pull_vec1 and pull_vec2) with +x and -x values and that does not even pull the protein I tried using only pull_group1 and pull_group2, without a reference, and neither groups get pulled. I chose different references, I do have some success but I don't think it is the best way to do it. How do I pull the N and C terminal apart, by simultaneously pulling them in opposite directions?Why is my vector definition wrong? This is my pull code: pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 2 pull_group0 = Chain-C pull_group1 = Chain-B pull_group2 = Chain-A %pull_vec1 = -31 0 0 %pull_vec2 = 31 0 0 I suspect the % signs will mess things up, but probably will give a fatal error, if nothing else. pull_rate1 = 0.002 pull_k1 = 1000 pull_rate2 = 0.002 pull_k2 = 1000 Here's the problem. You're telling the two pulled groups to move in the same direction. With distance geometry, the selections are a bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the groups will be pulled in opposite directions. Otherwise, you're just towing your protein along in the box. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Hi, Thanks for the reply! I tried the rates, and only the terminal with positive rate gets pulled. The first and the last amino acids are spatially oriented one behind the other. I think defining a vector might work better, but I am not sure why nothing happens when I define a pull_vec1 and pull_vec2. Am I missing anything? Thanks, Sai On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Janani Ganesan wrote: Hi, I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it. I define a different vector (pull_vec1 and pull_vec2) with +x and -x values and that does not even pull the protein I tried using only pull_group1 and pull_group2, without a reference, and neither groups get pulled. I chose different references, I do have some success but I don't think it is the best way to do it. How do I pull the N and C terminal apart, by simultaneously pulling them in opposite directions?Why is my vector definition wrong? This is my pull code: pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 2 pull_group0 = Chain-C pull_group1 = Chain-B pull_group2 = Chain-A %pull_vec1 = -31 0 0 %pull_vec2 = 31 0 0 I suspect the % signs will mess things up, but probably will give a fatal error, if nothing else. pull_rate1 = 0.002pull_k1 = 1000pull_rate2 = 0.002 pull_k2 = 1000 Here's the problem. You're telling the two pulled groups to move in the same direction. With distance geometry, the selections are a bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the groups will be pulled in opposite directions. Otherwise, you're just towing your protein along in the box. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *Every sentence I utter must be understood not as an affirmation but as a question. - Niels Bohr* -- 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] (no subject)
Sai Janani Ganesan wrote: Hi, Thanks for the reply! I tried the rates, and only the terminal with positive rate gets pulled. The first and the last amino acids are spatially oriented one behind the other. I think defining a vector might work better, but I am not sure why nothing happens when I define a pull_vec1 and pull_vec2. Am I missing anything? When setting distance as the pull_geometry, only pull_dim is used; pull_vec is ignored. If you want to define vectors, use the direction pull_geometry. -Justin Thanks, Sai On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Janani Ganesan wrote: Hi, I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it. I define a different vector (pull_vec1 and pull_vec2) with +x and -x values and that does not even pull the protein I tried using only pull_group1 and pull_group2, without a reference, and neither groups get pulled. I chose different references, I do have some success but I don't think it is the best way to do it. How do I pull the N and C terminal apart, by simultaneously pulling them in opposite directions?Why is my vector definition wrong? This is my pull code: pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 2 pull_group0 = Chain-C pull_group1 = Chain-B pull_group2 = Chain-A %pull_vec1 = -31 0 0 %pull_vec2 = 31 0 0 I suspect the % signs will mess things up, but probably will give a fatal error, if nothing else. pull_rate1 = 0.002pull_k1 = 1000pull_rate2 = 0.002 pull_k2 = 1000 Here's the problem. You're telling the two pulled groups to move in the same direction. With distance geometry, the selections are a bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the groups will be pulled in opposite directions. Otherwise, you're just towing your protein along in the box. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- /Every sentence I utter must be understood not as an affirmation but as a question. - Niels Bohr/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
On 27/09/2011 11:04 PM, Prema Awati wrote: Hi, Thanks for your suggestion; I am attaching the vac plot for short time interval ; Please let me know whether its correct or not. regards. Atoms are colliding over a time scale not that much larger than the integration time step (else you'd probably use a larger time step), and the velocities change during collisions, so the characteristic times of velocity autocorrelation are going to be not that much larger than the integration time step. To measure how velocities correlate with themselves, you need to make observations smaller than that characteristic time. Your graph suggests you collected data every 5ps (maybe every 2500 integration steps?), and shows that there is little self-correlation at or beyond 5ps, which is what you might have expected. 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
Re: [gmx-users] (no subject)
Алексей Раевский wrote: Hi. I've look through the manual and didn't find an answer on my question: i've got a trajectory and i want to convert it in *.pdb with such parameters of index file [all atoms within a sphere with a chosen radius around selected atom]. What can i do? Thank you Use g_select to generate the index group and trjconv to write the file in the format (and with the contents) that you want. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Joschua Sterzenbach wrote: Hi what do I need for a md with gromacs? I made a tutorial in which I download an example file, but what I I don't have such a file downloaded from the pdb? What do I need to create a first input file? To run a simulation, you need coordinates (.gro,.pdb, etc), a topology (.top), and instructions to run the simulation (.mdp). Start with getting your coordinate file: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources The follow a suitable workflow to add whatever else you need in the system and run it: http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Nilesh Dhumal wrote: Hello, I want to simulate system with 128 ionic liquids (128 cation+128 anion). I have made a pdb file with a single ionic liquids ion pairs. How can I genrate 128 ion pairs using single ion pair .pdb file. You can use genconf -nbox to generate a grid of replicates, but this artificially ordered system will need an extremely long equilibration time. You can induce some randomness to the system with genconf -rot. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Janowicz, Adrianna C. wrote: I'm trying to install gromacs-3.3 am constantly getting errors regarding configure: error: C++ preprocessor /lib/cpp fails sanity check or CC non executable. Is this because my version of Linux is too new because these errors were not happening when I installed the newest versions of Gromacs? There may be some incompatibility, but it's hard to say without more details. Is there any particular reason you're trying to install an ancient Gromacs version? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions, you're going to be undoing work you thought you did. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions, you're going to be undoing work you thought you did. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] (no subject)
Sara baretller wrote: Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Please copy and paste the exact (pertinent) output from the log file. -Justin Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions, you're going to be undoing work you thought you did. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Hi this a part of the md.log where the system has -50 charge two-body bonded interactions: 0.407 nm, Bond, atoms 514 515 multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275 Minimum cell size due to bonded interactions: 0.804 nm Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm Estimated maximum distance required for P-LINCS: 0.810 nm This distance will limit the DD cell size, you can override this with -rcon Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm The maximum allowed number of cells is: X 11 Y 11 Z 11 Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: -50.000 Generated table with 1100 data points for Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Shift. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Please copy and paste the exact (pertinent) output from the log file. -Justin Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions, you're going to be undoing work you thought you did. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] (no subject)
Sara baretller wrote: Hi this a part of the md.log where the system has -50 charge two-body bonded interactions: 0.407 nm, Bond, atoms 514 515 multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275 Minimum cell size due to bonded interactions: 0.804 nm Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm Estimated maximum distance required for P-LINCS: 0.810 nm This distance will limit the DD cell size, you can override this with -rcon Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm The maximum allowed number of cells is: X 11 Y 11 Z 11 Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: -50.000 Generated table with 1100 data points for Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Shift. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present There's nothing abnormal here. genion reports that it finds a -50 charge on the system. That's what it's supposed to do. Based on what it finds in the topology, it adds neutralizing ions and any additional ions to reach the specified concentration. You only have a problem if grompp later complains that there's still some residual charge (excluding tiny rounding discrepancies). -Justin On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Please copy and paste the exact (pertinent) output from the log file. -Justin Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions, you're going to be undoing work you thought you did. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] (no subject)
thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 -neutral -o file.gro -random does not neutralize the system to 0 . On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: Hi this a part of the md.log where the system has -50 charge two-body bonded interactions: 0.407 nm, Bond, atoms 514 515 multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275 Minimum cell size due to bonded interactions: 0.804 nm Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm Estimated maximum distance required for P-LINCS: 0.810 nm This distance will limit the DD cell size, you can override this with -rcon Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm The maximum allowed number of cells is: X 11 Y 11 Z 11 Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: -50.000 Generated table with 1100 data points for Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Shift. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present There's nothing abnormal here. genion reports that it finds a -50 charge on the system. That's what it's supposed to do. Based on what it finds in the topology, it adds neutralizing ions and any additional ions to reach the specified concentration. You only have a problem if grompp later complains that there's still some residual charge (excluding tiny rounding discrepancies). -Justin On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Sara baretller wrote: Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Please copy and paste the exact (pertinent) output from the log file. -Justin Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions, you're going to be undoing work you thought you did. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] (no subject)
You are not specifying the ions to be added using the -pname and -nname options with the genion command. Perhaps that is a problem? Warren Gallin On 2011-07-26, at 2:49 PM, Sara baretller wrote: thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 -neutral -o file.gro -random does not neutralize the system to 0 . On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: Hi this a part of the md.log where the system has -50 charge two-body bonded interactions: 0.407 nm, Bond, atoms 514 515 multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275 Minimum cell size due to bonded interactions: 0.804 nm Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm Estimated maximum distance required for P-LINCS: 0.810 nm This distance will limit the DD cell size, you can override this with -rcon Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm The maximum allowed number of cells is: X 11 Y 11 Z 11 Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: -50.000 Generated table with 1100 data points for Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Shift. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present There's nothing abnormal here. genion reports that it finds a -50 charge on the system. That's what it's supposed to do. Based on what it finds in the topology, it adds neutralizing ions and any additional ions to reach the specified concentration. You only have a problem if grompp later complains that there's still some residual charge (excluding tiny rounding discrepancies). -Justin On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Please copy and paste the exact (pertinent) output from the log file. -Justin Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions, you're going to be undoing work you thought you did. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] (no subject)
Warren Gallin wrote: You are not specifying the ions to be added using the -pname and -nname options with the genion command. Perhaps that is a problem? They are not necessary; the default names are used and should be correct for all force fields now that naming has been standardized. Thus far I have seen no evidence that genion is not doing what it is supposed to. It reports finding a net -50 charge on the system. What happens then? Does the output coordinate file contain ions? The topology will not be modified because genion is not being told to (i.e. through the use of -p). -Justin Warren Gallin On 2011-07-26, at 2:49 PM, Sara baretller wrote: thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 -neutral -o file.gro -random does not neutralize the system to 0 . On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: Hi this a part of the md.log where the system has -50 charge two-body bonded interactions: 0.407 nm, Bond, atoms 514 515 multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275 Minimum cell size due to bonded interactions: 0.804 nm Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm Estimated maximum distance required for P-LINCS: 0.810 nm This distance will limit the DD cell size, you can override this with -rcon Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm The maximum allowed number of cells is: X 11 Y 11 Z 11 Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: -50.000 Generated table with 1100 data points for Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Shift. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present There's nothing abnormal here. genion reports that it finds a -50 charge on the system. That's what it's supposed to do. Based on what it finds in the topology, it adds neutralizing ions and any additional ions to reach the specified concentration. You only have a problem if grompp later complains that there's still some residual charge (excluding tiny rounding discrepancies). -Justin On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Please copy and paste the exact (pertinent) output from the log file. -Justin Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions, you're going to be undoing work you thought you did. -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu
Re: [gmx-users] (no subject)
hi all yes the gro file does have all ions, NA + number of ions equal to CL number. so when i use grep command , i have same number of NA and CL and that what tells me that something is wrong , because i should have another 50 ions of NA extra to neutralize the system Thank you On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Warren Gallin wrote: You are not specifying the ions to be added using the -pname and -nname options with the genion command. Perhaps that is a problem? They are not necessary; the default names are used and should be correct for all force fields now that naming has been standardized. Thus far I have seen no evidence that genion is not doing what it is supposed to. It reports finding a net -50 charge on the system. What happens then? Does the output coordinate file contain ions? The topology will not be modified because genion is not being told to (i.e. through the use of -p). -Justin Warren Gallin On 2011-07-26, at 2:49 PM, Sara baretller wrote: thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 -neutral -o file.gro -random does not neutralize the system to 0 . On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: Hi this a part of the md.log where the system has -50 charge two-body bonded interactions: 0.407 nm, Bond, atoms 514 515 multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275 Minimum cell size due to bonded interactions: 0.804 nm Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm Estimated maximum distance required for P-LINCS: 0.810 nm This distance will limit the DD cell size, you can override this with -rcon Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm The maximum allowed number of cells is: X 11 Y 11 Z 11 Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: -50.000 Generated table with 1100 data points for Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Shift. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present There's nothing abnormal here. genion reports that it finds a -50 charge on the system. That's what it's supposed to do. Based on what it finds in the topology, it adds neutralizing ions and any additional ions to reach the specified concentration. You only have a problem if grompp later complains that there's still some residual charge (excluding tiny rounding discrepancies). -Justin On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Sara baretller wrote: Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Please copy and paste the exact (pertinent) output from the log file. -Justin Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi all I used the genion to add a concentration and to neutalize the system in the same time by using the *genion -s file.tpr -conc 0.2 -neutral -o file.gro -random so it did add the NA and Cl but it did not neutralize the system, the net charge of the system still the same negative. I find this hard to believe. The application of genion -conc -neutral has worked in every instance I've tried it along every Gromacs version. Check your output again. so i tried to use the genion seperate to neutralize the charge using the file.tpr and out file as the file.gro, however it reset the file.gro and i lose the NA And CL ions added for the concentration. Without the actual sequence of commands, this is not a useful description. genion adds ions based on whatever it finds in the .tpr file (which is presumably not neutralized). If you do not re-create a .tpr file in between different additions of ions,
Re: [gmx-users] (no subject)
Sara baretller wrote: hi all yes the gro file does have all ions, NA + number of ions equal to CL number. so when i use grep command , i have same number of NA and CL and that what tells me that something is wrong , because i should have another 50 ions of NA extra to neutralize the system I've never seen genion do anything like this. If you send me your .tpr file (off-list) I will see if I can uncover what's going on. I also need to know which Gromacs version you're using. -Justin Thank you On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Warren Gallin wrote: You are not specifying the ions to be added using the -pname and -nname options with the genion command. Perhaps that is a problem? They are not necessary; the default names are used and should be correct for all force fields now that naming has been standardized. Thus far I have seen no evidence that genion is not doing what it is supposed to. It reports finding a net -50 charge on the system. What happens then? Does the output coordinate file contain ions? The topology will not be modified because genion is not being told to (i.e. through the use of -p). -Justin Warren Gallin On 2011-07-26, at 2:49 PM, Sara baretller wrote: thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2 -neutral -o file.gro -random does not neutralize the system to 0 . On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi this a part of the md.log where the system has -50 charge two-body bonded interactions: 0.407 nm, Bond, atoms 514 515 multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275 Minimum cell size due to bonded interactions: 0.804 nm Maximum distance for 9 constraints, at 120 deg. angles, all-trans: 0.810 nm Estimated maximum distance required for P-LINCS: 0.810 nm This distance will limit the DD cell size, you can override this with -rcon Optimizing the DD grid for 4 cells with a minimum initial size of 0.810 nm The maximum allowed number of cells is: X 11 Y 11 Z 11 Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: -50.000 Generated table with 1100 data points for Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Shift. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing ia32 SSE2 support... present There's nothing abnormal here. genion reports that it finds a -50 charge on the system. That's what it's supposed to do. Based on what it finds in the topology, it adds neutralizing ions and any additional ions to reach the specified concentration. You only have a problem if grompp later complains that there's still some residual charge (excluding tiny rounding discrepancies). -Justin On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi All I used the genion command using like this genion -s file.tpr -conc 0.2 -neutral -o file.gro -random again and i checked the md.log file and it says that the net charge is negative like it was before using the genion command. so can anybody tell me what is wrong with the line genion -s file.tpr -conc 0.2 -neutral -o file.gro -random . Please copy and paste the exact (pertinent) output from the log file. -Justin Sara On Tue, Jul 26, 2011 at 1:05 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu
Re: [gmx-users] (no subject)
Sara baretller wrote: Hi All I have a question about adding ions to the system. using Genion one can add ions but how can you convert molecule/mol to number of molecules or ions ?? let say 2 e 23 molecule/mol to X number of molecule or ions Use Avogadro's number. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
yes i had X M and i convert it to X molecule / mol using Avogadro's number. but how do i get only molecules or ions On Fri, Jul 15, 2011 at 1:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: Hi All I have a question about adding ions to the system. using Genion one can add ions but how can you convert molecule/mol to number of molecules or ions ?? let say 2 e 23 molecule/mol to X number of molecule or ions Use Avogadro's number. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] (no subject)
Sara baretller wrote: yes i had X M and i convert it to X molecule / mol using Avogadro's number. but how do i get only molecules or ions I'm not following your notation. If you've got a given concentration (mol/L), you obtain molecules/L by using Avogadro's number. Then just multiply by the volume of the box to get the number of molecules or ions. -Justin On Fri, Jul 15, 2011 at 1:52 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: Hi All I have a question about adding ions to the system. using Genion one can add ions but how can you convert molecule/mol to number of molecules or ions ?? let say 2 e 23 molecule/mol to X number of molecule or ions Use Avogadro's number. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Seibold, Stephen wrote: I am sorry if this is a simple question, but I have spent the better part of the day attempting to figure it out using gromacs mailing list..etc.. Here is the problem. When I attempt to run genbox my output produces the error that spc216.gro cannot be found in your GMXLIB path. Here is what I've done. My bashrc_profile has the following A file called bashrc_profile is not going to do anything unless you explicitly source it yourself. Default files that are read are called .bashrc or .bash_profile. -Justin .. ... export LD_LIBRARY_PATH=/usr/local/lib export GMXLIB=/usr/local/gromacs/share/gromacs/top source /usr/local/gromacs/bin/GMXRC ... I have checked and spc216.gro is in /usr/local/gromacs/share/gromacs/top The ff is found by pdb2gmx which is in the same location Can someone please help me? -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
thank you for your help, will it be alot to add 700 ions to a system made of water and proteins that is 4000 molecules -- 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] (no subject)
Sara baretller wrote: thank you for your help, will it be alot to add 700 ions to a system made of water and proteins that is 4000 molecules That would certainly be an extraordinarily high concentration. What is your target molarity? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
between 2.2 and 2.7 M. Thank you On Fri, Jul 15, 2011 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sara baretller wrote: thank you for your help, will it be alot to add 700 ions to a system made of water and proteins that is 4000 molecules That would certainly be an extraordinarily high concentration. What is your target molarity? -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] (no subject)
Sara baretller wrote: between 2.2 and 2.7 M. Well, double check your work. Your previous post contained several units that made no sense, so I don't know if you've done the calculations correctly. For adding ions, just use genion -conc and it will do the work for you. That way, you'll know if you're right. -Justin Thank you On Fri, Jul 15, 2011 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: thank you for your help, will it be alot to add 700 ions to a system made of water and proteins that is 4000 molecules That would certainly be an extraordinarily high concentration. What is your target molarity? -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
thumbs up per tuti On Jul 15, 2011, at 6:23 PM, Justin A. Lemkul wrote: Sara baretller wrote: between 2.2 and 2.7 M. Well, double check your work. Your previous post contained several units that made no sense, so I don't know if you've done the calculations correctly. For adding ions, just use genion -conc and it will do the work for you. That way, you'll know if you're right. -Justin Thank you On Fri, Jul 15, 2011 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sara baretller wrote: thank you for your help, will it be alot to add 700 ions to a system made of water and proteins that is 4000 molecules That would certainly be an extraordinarily high concentration. What is your target molarity? -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- 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
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arezoo rahmanpour wrote: Hi, Upon running g_helix_d -s md.tpr -n md.ndx -f md.trr I got the following output: Fatal error: rnr==0. Please tell me how can I proceed? The error indicates that g_helix has identified zero residues on which it can operate. Most likely whatever index group you've selected is not suitable for the analysis. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Sven Benson wrote: Hello everybody, I was wondering if the gro file format somehow supports systems that are greater than 9 molecules (not atoms), since the first column is fixed to size 5. Anybody know a way around this problem? I've tried working with pdb, but GROMACS seems to ignore all entries with atom numbers larger than 9 atoms in this format as well. What command is ignoring atoms? I've never had problems with systems 99,999 atoms. At 100,000 the numbers start over from zero, but you can still make index files that will then contain proper atom numbers (100,000 and beyond). -Justin Anybody know a way around this problem? I'd appreciate any helpful pointers. Cheers Sven -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
On 26/05/2011 2:55 PM, Ravi Kumar Venkatraman wrote: Dear Sir/Madam, In gromacs tutor we have water .gro file for spc potential. How to get .gro files from spc216.pdb of different potentials like tip3p tip4p ... etc. You don't need a file in .gro format, and coordinate files for any of the three-point water models are interchangeable. There are other files in $GMXLIB/share/top for the other water models. 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
Re: [gmx-users] (no subject)
Алексей Раевский wrote: Hi, I have got a situation and I don't know how to cope with it. I carried out a simulation in gromacs 4.5.3 and the objects are protein, rna, water...The idea is that one atom part of rna has to create an h-bond with a water molecule, which at the same time makes h-bonds with aminoacids of the binding site. Something like a coordination molecule. So a command g_dist with index file and distance 0.35 showed me a number of water molecule I needed. But when I decided to visualize this process I saw that my protein with rna went out from the water box to another cell and the part of rna sppeared in the bottom of this box (( as I know this is not a bug or error of pbc. But i don't understand what is happening. Does my water forms bonds with this part and aminoacids (!!!) of binding site, because when I've converted trr to pdb with index file (atoms of binding site, part of rna, water molecules I've got with g_dist) I saw water molecules with part of rna in the bottom of display and binding site in the top...I tried to use -pbc nojump and center, -pbc mol...this flags united protein, rna and part of rna togetrher, but my water is not there Thank you For proper visualization, there is a workflow here: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions For complex systems, multiple iterations of trjconv are almost certainly required, some or all of which might need custom index groups. Bridging and simultaneous hydrogen bonds have been discussed frequently in the last few weeks. Have a look through the list archive. g_dist and g_hbond are the proper tools, but multiple operations and your own post-processing of such data will be required to extract the information you need. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
trevor brown wrote: Dear Justin/Mark, I would like to have a private course about Gromacs in Holland. Is there such a facility for this? Who should I talk with? Can't help you there. I'm in the U.S. Or is there a workshop in near future? Any workshops will surely be announced on the list, but there haven't been any Gromacs-specific ones for several years. -Justin best wishes -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
trevor brown wrote: Dear users, How can we fix the position of some atoms? Use position restraints or freeze groups. -Justin best wishes trevor -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
On 01/20/11, a...@rri.res.in wrote: Dear gmx users, Can anyone please help me out with the commands used for finding the pair correlation function of the water molecules with respect to the C alpha atom of the protein and reorientational time correlation function of the water.?? Yes. GROMACS comes with dozens of utility programs, which are grouped by category in section 7.4, discussed in the next chapter, and described individually in detail in the appendices. Do look in those places first before emailing the list - it will be faster and you'll learn more. 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
Re: [gmx-users] (no subject)
harpreet singh wrote: Dear Gromacs users, I want to study the thermostability of a protein using MD simulations. I will be thankful if someone could guide me to do this job. Your request is too broad to be properly addressed on a list like this one. No one is going to do your work for you. High-temperature MD has been performed for many years. Do some reading and come back with specific technical questions if and when they arise. -Justin Regards Harpreet Singh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
Quoting Olga Ivchenko olga.ivche...@gmail.com: Dear gromacs users, I want to heat system from 0K till 300K. Than do equilibration dynamics in water. I can not find any .mdp files where the system is gradually heated from initial temperature (0K) till needed temperature. I can only find NVP and NVT equilibration dynamics. Please can you advice me on this? Please read in the manual about simulated annealing. There is even an example in the online manual (manual.gromacs.org). -Justin best, Olga Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
mustafa bilsel wrote: Hi, when I tried to make energy minimisation, I see following error. My parameters are at the end of the email. What should I do? Fatal error: Atomtype HW not found More pertinent information would be a description of your system, which force field you're using, as well as which water model you are using. The error comes from a mismatch between these latter two items. HW is a water hydrogen for most force fields, but the Gromos96 series use H. I suspect you've mangled the topology in some way such that you've broken the internal mechanics of whatever force field you're using. -Justin Best wishes Mustafa MY EM.MDP integrator= steep nsteps=200 nstlist=10 rlist=1.0 coulombtype=pme rcoulomb=1.0 vdw_type=cut-off rvdw=1.0 nstenergy=10 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
On 28/10/2010 2:24 AM, Nilesh Dhumal wrote: Thanks a lot. I made some changes in topology file for rerun simulation. Still I am getting same potential energy. If topology files are different then why the potential energy is same? Occam's razor says that the topologies are not (meaningfully) different. Check your command lines, and compare your .tpr files with gmxcheck. Mark Nilesh On Tue, October 26, 2010 4:29 pm, Mark Abraham wrote: - Original Message - From: Nilesh Dhumalndhu...@andrew.cmu.edu Date: Wednesday, October 27, 2010 1:04 Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS usersgmx-users@gromacs.org I used the same .tpr file. I added -dlb yes and - reprod yes during mdrun with rerun option. Still I am not geting why energy, temp, pressure are changing since I have same topology file and .trr file. As I said last time, a parallel rerun cannot reproduce a run unless they're both run under the same conditions. Changing the options for the rerun cannot achieve this, because the original run probably had dynamic load balancing. Mark Is there any bug in rerun option? Nilesh On Mon, October 25, 2010 8:50 pm, Mark Abraham wrote: - Original Message - From: Nilesh Dhumalndhu...@andrew.cmu.edu Date: Tuesday, October 26, 2010 10:50 Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS usersgmx-users@gromacs.org I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb - p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6- 128.pdb - p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total energy varies between +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectory. Why the total energy is not constant. Those .tpr should be identical - but you can check that with gmxcheck. Reruns do neighbour-searching every step, whereas your normal simulation followed the nstlist setting. That's part of why my earlier advice suggested doing reruns for each simulation you wish to compare. You should be able to get good/better agreement for steps where nstlist directed neighbour-searching in the original run. Also, whether or not constraints have been applied (and when!) could influence the energies to about this degree. I don't recall the details here. Even once you've removed all algorithm-specific sources of difference, there are other sources of non-reproducibility, such as the assignment of particles to DD cells. Your original mdrun probably used dynamic load-balancing, and that cannot be reproduced in the DD used by the rerun. (Or indeed by a repeat of your original mdrun!) Setting -dlb no in the original simulation might be enough to get agreement here, or maybe mdrun -reprod will be required. Mark NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. 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
Re: [gmx-users] (no subject)
I used the same .tpr file. I added -dlb yes and -reprod yes during mdrun with rerun option. Still I am not geting why energy, temp, pressure are changing since I have same topology file and .trr file. Is there any bug in rerun option? Nilesh On Mon, October 25, 2010 8:50 pm, Mark Abraham wrote: - Original Message - From: Nilesh Dhumal ndhu...@andrew.cmu.edu Date: Tuesday, October 26, 2010 10:50 Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS users gmx-users@gromacs.org I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb - p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6-128.pdb - p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total energy varies between +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectory. Why the total energy is not constant. Those .tpr should be identical - but you can check that with gmxcheck. Reruns do neighbour-searching every step, whereas your normal simulation followed the nstlist setting. That's part of why my earlier advice suggested doing reruns for each simulation you wish to compare. You should be able to get good/better agreement for steps where nstlist directed neighbour-searching in the original run. Also, whether or not constraints have been applied (and when!) could influence the energies to about this degree. I don't recall the details here. Even once you've removed all algorithm-specific sources of difference, there are other sources of non-reproducibility, such as the assignment of particles to DD cells. Your original mdrun probably used dynamic load-balancing, and that cannot be reproduced in the DD used by the rerun. (Or indeed by a repeat of your original mdrun!) Setting -dlb no in the original simulation might be enough to get agreement here, or maybe mdrun -reprod will be required. Mark NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. 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 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
Re: [gmx-users] (no subject)
- Original Message - From: Nilesh Dhumal ndhu...@andrew.cmu.edu Date: Wednesday, October 27, 2010 1:04 Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS users gmx-users@gromacs.org I used the same .tpr file. I added -dlb yes and - reprod yes during mdrun with rerun option. Still I am not geting why energy, temp, pressure are changing since I have same topology file and .trr file. As I said last time, a parallel rerun cannot reproduce a run unless they're both run under the same conditions. Changing the options for the rerun cannot achieve this, because the original run probably had dynamic load balancing. Mark Is there any bug in rerun option? Nilesh On Mon, October 25, 2010 8:50 pm, Mark Abraham wrote: - Original Message - From: Nilesh Dhumal ndhu...@andrew.cmu.edu Date: Tuesday, October 26, 2010 10:50 Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS users gmx-users@gromacs.org I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb - p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6- 128.pdb - p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total energy varies between +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectory. Why the total energy is not constant. Those .tpr should be identical - but you can check that with gmxcheck. Reruns do neighbour-searching every step, whereas your normal simulation followed the nstlist setting. That's part of why my earlier advice suggested doing reruns for each simulation you wish to compare. You should be able to get good/better agreement for steps where nstlist directed neighbour-searching in the original run. Also, whether or not constraints have been applied (and when!) could influence the energies to about this degree. I don't recall the details here. Even once you've removed all algorithm-specific sources of difference, there are other sources of non-reproducibility, such as the assignment of particles to DD cells. Your original mdrun probably used dynamic load-balancing, and that cannot be reproduced in the DD used by the rerun. (Or indeed by a repeat of your original mdrun!) Setting -dlb no in the original simulation might be enough to get agreement here, or maybe mdrun -reprod will be required. Mark NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. 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
Re: [gmx-users] (no subject)
I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log rm -f *#* I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total enregy vaies beteen +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectroy. Why the total energy is not contant. NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. 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
Re: [gmx-users] (no subject)
I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total energy varies between +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectory. Why the total energy is not constant. NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. 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
Re: [gmx-users] (no subject)
- Original Message - From: Nilesh Dhumal ndhu...@andrew.cmu.edu Date: Tuesday, October 26, 2010 10:50 Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS users gmx-users@gromacs.org I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb - p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6-128.pdb - p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total energy varies between +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectory. Why the total energy is not constant. Those .tpr should be identical - but you can check that with gmxcheck. Reruns do neighbour-searching every step, whereas your normal simulation followed the nstlist setting. That's part of why my earlier advice suggested doing reruns for each simulation you wish to compare. You should be able to get good/better agreement for steps where nstlist directed neighbour-searching in the original run. Also, whether or not constraints have been applied (and when!) could influence the energies to about this degree. I don't recall the details here. Even once you've removed all algorithm-specific sources of difference, there are other sources of non-reproducibility, such as the assignment of particles to DD cells. Your original mdrun probably used dynamic load-balancing, and that cannot be reproduced in the DD used by the rerun. (Or indeed by a repeat of your original mdrun!) Setting -dlb no in the original simulation might be enough to get agreement here, or maybe mdrun -reprod will be required. Mark NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. 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 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] (no subject)
On 21/10/2010 11:55 PM, Nilesh Dhumal wrote: Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to calculate the energy for each step with and with out charge on solute simultaneously. Pl. help me solve this problem. I don't understand what you want to do. 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
Re: [gmx-users] (no subject)
I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. NIlesh On Thu, October 21, 2010 10:03 am, Mark Abraham wrote: On 21/10/2010 11:55 PM, Nilesh Dhumal wrote: Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to calculate the energy for each step with and with out charge on solute simultaneously. Pl. help me solve this problem. I don't understand what you want to do. 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
Re: [gmx-users] (no subject)
Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. You can't. Probably the best option is to do an mdrun -rerun using the second topology. -Justin NIlesh On Thu, October 21, 2010 10:03 am, Mark Abraham wrote: On 21/10/2010 11:55 PM, Nilesh Dhumal wrote: Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to calculate the energy for each step with and with out charge on solute simultaneously. Pl. help me solve this problem. I don't understand what you want to do. 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] (no subject)
On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. 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
Re: [gmx-users] (no subject)
Hi Prabha, Why did you choose that force field, and what CA atom type? Tsjerk On Thu, Sep 2, 2010 at 1:30 PM, praba vathy sumipraba2...@gmail.com wrote: Dear Sir, We have chosen force field Gromos96 53A6 parameter set. In that forcefield, how we add this CA atom type. Prabha -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
This is probably not intended for the list; it pertains directly to my membrane tutorial and is likely a result of choosing the force field incorrectly or not properly incorporating the lipid parameters as instructed. -Justin Tsjerk Wassenaar wrote: Hi Prabha, Why did you choose that force field, and what CA atom type? Tsjerk On Thu, Sep 2, 2010 at 1:30 PM, praba vathy sumipraba2...@gmail.com wrote: Dear Sir, We have chosen force field Gromos96 53A6 parameter set. In that forcefield, how we add this CA atom type. Prabha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
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Anitha wrote: I executed the following command. g_sas -s topol.tpr -f traj.xtc -or resarea.xvg -o area.xvg xmgrace -nxy resarea.xvg I have chosen the protein group for surface calculation and output. I get two sets of values: one is bigger (black) than the other (red). I have checked the manual and other sources, but I could not find an answer about the black and red line. What does red and black line shows? Read the headers of the .xvg file. -Justin -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
In the headers file also i didn`t get the answer about those lines On Fri, Jul 30, 2010 at 4:01 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anitha wrote: I executed the following command. g_sas -s topol.tpr -f traj.xtc -or resarea.xvg -o area.xvg xmgrace -nxy resarea.xvg I have chosen the protein group for surface calculation and output. I get two sets of values: one is bigger (black) than the other (red). I have checked the manual and other sources, but I could not find an answer about the black and red line. What does red and black line shows? Read the headers of the .xvg file. -Justin -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php -- S.Anitha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
Anitha wrote: In the headers file also i didn`t get the answer about those lines Well, what do they say? -Justin On Fri, Jul 30, 2010 at 4:01 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anitha wrote: I executed the following command. g_sas -s topol.tpr -f traj.xtc -or resarea.xvg -o area.xvg xmgrace -nxy resarea.xvg I have chosen the protein group for surface calculation and output. I get two sets of values: one is bigger (black) than the other (red). I have checked the manual and other sources, but I could not find an answer about the black and red line. What does red and black line shows? Read the headers of the .xvg file. -Justin -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
my header starts as # g_sas is part of G R O M A C S: # # GROtesk MACabre and Sinister # @title Area per residue @xaxis label Residue @yaxis label Area (nm\S2\N) @TYPE xy 10.846565 0.312334 2 0.598 0.189911 30.837035 0.363443 4 1.14936 0.304359 50.630063 0.233607 60.625571 0.321569 70.261401 0.240533 8 0.0940011 0.0872611 i`m not able to understand what the second and third column represents On Fri, Jul 30, 2010 at 4:33 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anitha wrote: In the headers file also i didn`t get the answer about those lines Well, what do they say? -Justin On Fri, Jul 30, 2010 at 4:01 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Anitha wrote: I executed the following command. g_sas -s topol.tpr -f traj.xtc -or resarea.xvg -o area.xvg xmgrace -nxy resarea.xvg I have chosen the protein group for surface calculation and output. I get two sets of values: one is bigger (black) than the other (red). I have checked the manual and other sources, but I could not find an answer about the black and red line. What does red and black line shows? Read the headers of the .xvg file. -Justin -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php -- S.Anitha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
Anitha wrote: my header starts as # g_sas is part of G R O M A C S: # # GROtesk MACabre and Sinister # @title Area per residue @xaxis label Residue @yaxis label Area (nm\S2\N) @TYPE xy 10.846565 0.312334 2 0.598 0.189911 30.837035 0.363443 4 1.14936 0.304359 50.630063 0.233607 60.625571 0.321569 70.261401 0.240533 8 0.0940011 0.0872611 i`m not able to understand what the second and third column represents This is a plot of surface area per residue, and as the y-axis label indicates, you have area in square nm. The second column is the area, the third column is the fluctuation. The last column is not immediately obvious, but from the code it is clear (and an identical question posted to this list not too long ago). -Justin On Fri, Jul 30, 2010 at 4:33 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anitha wrote: In the headers file also i didn`t get the answer about those lines Well, what do they say? -Justin On Fri, Jul 30, 2010 at 4:01 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anitha wrote: I executed the following command. g_sas -s topol.tpr -f traj.xtc -or resarea.xvg -o area.xvg xmgrace -nxy resarea.xvg I have chosen the protein group for surface calculation and output. I get two sets of values: one is bigger (black) than the other (red). I have checked the manual and other sources, but I could not find an answer about the black and red line. What does red and black line shows? Read the headers of the .xvg file. -Justin -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- S.Anitha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
munu...@yahoo.com wrote: Hi, I am studying polyglutamine regarding to my Ph.D work. Now my sequence is NH3+ -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-COO-. I would like to cap the N and C terminal with the protecting groups CH3CO and NHCH3 instead of NH3+ and COO- respectively (i.e. CH3CONH-Q-Q-Q-Q-Q-CONHCH3). I am using GROMACS software for this study. I have tried with GROMACS but its library has not been included with N Acety and N Methylamide at its N and C terminal. Due to this .gro file or .top file could not be made. I have even included the CH3CO group in the library. still it is not making sense to produce the .gro and .top file. I request you to suggest how to cap the above thereby to overcome this problem using GROMACS. Most force fields include capping groups. You'll have to tell us exactly which force field you're trying to use, what files you modified (and with what), any relevant commands, errors, etc otherwise you'll get no useful advice. -Justin M. Baskar, Dept of Biophysics, Panjab University, Chandigarh, India. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
On 7/14/10 9:44 PM, munu...@yahoo.com wrote: Hi How do I built the terminals of a peptide withe ACE and NHMe i.e.CH3CO and NHCH3 respectively. please suggest. My sequence is -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q- M. Baskar. just add an extra residue (e.g. gly or ala) at eeither end using pymol or so, and then rename them in a text editor and throw away superfluous atoms. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
munu...@yahoo.com wrote: Hi How do I built the terminals of a peptide withe ACE and NHMe i.e.CH3CO and NHCH3 respectively. please suggest. My sequence is -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q- M. Baskar. http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources Note the last bullet point. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
munu...@yahoo.com wrote: Hi, I am using GROMACS 4.0 for simulating a peptide having 5 residues. I have built the sequence using pymol and capped the peptide with CH3CO and NHCH3 at its N and C terminal respectively and save in pdb file format. The pdb file was used to produce *.gro and *.top files using pdb2gmx ff G43a1 -ignh -f *.pdb -o *.gro -p *.top -ter. It has shown the option NH3+, NH2 and None. When choosing None it flashes error as well as not producing required files i.e. *.top and *.gro. Gromacs has library on NH3+, NH2, None and COO-, COOH, None at N and C terminal respectively. I have opened the file ff G43a1.rtp and I included the option CH3. Accordingly I have included in the files such as ffG43a1-n.tdb, ffG43a1-c.tdb, ffgmx.rtp, ffgmx-n.tdb and ffgmx-c.tdb which are responsible for making *.gro and *.top files. It flashes error the the atom CH3 in rsidue ACE 1 not found in rtp entry with 3 atoms while sorting atoms. Due to this I could not proceed further for simulating the peptides. The input *.pdb files is as: The atom name is CA, not CH3. The CH3 corresponds to the atom type. -Justin ATOM 1C ACE 1 -1.453 -2.461 -2.313 1.00 0.00 C ATOM 2O ACE 1 -1.746 -1.409 -2.895 1.00 0.00 O ATOM 3 CH3 ACE 1 -2.252 -3.727 -2.539 1.00 0.00 C ATOM 4 1HH3 ACE 1 -2.215 -4.006 -3.582 1.00 0.00 H ATOM 5 2HH3 ACE 1 -1.844 -4.532 -1.947 1.00 0.00 H ATOM 6 3HH3 ACE 1 -3.281 -3.569 -2.255 1.00 0.00 H ATOM 7 N GLN 2 -0.311 -2.482 -1.387 1.00 0.00 N ATOM 8 CAGLN 2 0.241-1.131 -1.387 1.00 0.00 C ATOM 9 C GLN 2 1.751-1.162 -1.387 1.00 0.00 C ATOM 10 O GLN 2 2.386-1.913 -0.650 1.00 0.00 O ATOM 11 CBGLN 2 -0.297-0.376 -0.151 1.00 0.00 C ATOM 12 CGGLN 2 0.152 1.115 -0.003 1.00 0.00 C ATOM 13 CDGLN 2 -0.293 1.910 1.231 1.00 0.00 C ATOM 14 NE2 GLN 2 -1.052 1.345 2.135 1.00 0.00 N ATOM 15 OE1 GLN 2 0.069 3.064 1.4021.00 0.00 O ATOM 16 H GLN 2 0.008-3.235 -0.883 1.00 0.00 H ATOM 17 HAGLN 2 -0.083-0.615 -2.310 1.00 0.00 H ATOM 18 2HB GLN 2 0.002-0.934 0.761 1.00 0.00 H ATOM 19 3HB GLN 2 -1.404-0.411 -0.164 1.00 0.00 H ATOM 20 2HG GLN 2 -0.150 1.693 -0.896 1.00 0.00 H ATOM 213HG GLN 2 1.255 1.185 0.008 1.00 0.00 H ATOM 221HE2 GLN 2 -1.249 1.921 2.955 1.00 0.00H ATOM 232HE2 GLN 2 -1.262 0.359 1.967 1.00 0.00H ATOM 24 N GLN 3 2.483 -0.268 -2.296 1.00 0.00N ATOM 25 CA GLN 3 3.901 -0.525 -2.069 1.00 0.00 C ATOM 26 C GLN 3 4.691 0.763 -2.064 1.00 0.00 C ATOM 27 O GLN 3 4.517 1.636 -2.911 1.00 0.00 O ATOM 28 CB GLN 3 4.413 -1.484 -3.166 1.00 0.00 C ATOM 29 CG GLN 3 5.913 -1.914 -3.062 1.00 0.00 C ATOM 30 CD GLN 3 6.509 -2.817 -4.150 1.00 0.00 C ATOM 31 NE2 GLN 3 5.759 -3.230 -5.140 1.00 0.00 N ATOM 32 OE1 GLN 3 7.686 -3.143 -4.125 1.00 0.00 O ATOM 33 H GLN 3 2.103 0.360 -2.916 1.00 0.00 H ATOM 34 HA GLN 3 4.022 -0.995 -1.075 1.00 0.00 H ATOM 35 2HB GLN 3 4.242 -1.011 -4.156 1.00 0.00 H ATOM 36 3HB GLN 3 3.784 -2.396 -3.166 1.00 0.00 H ATOM 37 2HG GLN 3 6.102 -2.402 -2.088 1.00 0.00 H ATOM 38 3HG GLN 3 6.569 -1.025 -3.054 1.00 0.00 H ATOM 39 1HE2 GLN 3 6.248 -3.772 -5.855 1.00 0.00 H ATOM 40 2HE2 GLN 3 4.804 -2.867 -5.139 1.00 0.00 H ATOM 41 N GLN 4 5.698 0.978 -1.015 1.00 0.00 N ATOM 42 CA GLN 4 6.284 2.289 -1.272 1.00 0.00 C ATOM 43 C GLN 4 7.779 2.267 -1.059 1.00 0.00 C ATOM 44 O GLN 4 8.372 1.247 -0.713 1.00 0.00 O ATOM 45 CB GLN 4 5.608 3.324 -0.346 1.00 0.00 C ATOM 46 CG GLN 4 6.077 4.808 -0.510 1.00 0.00 C ATOM 47 CD GLN 4 5.494 5.882 0.418 1.00 0.00 C ATOM 48 NE2 GLN 4 4.606 5.555 1.321 1.00 0.00 N ATOM 49 OE1 GLN 4 5.864 7.044 0.347 1.00 0.00 O ATOM 50 H GLN 4 5.925 0.375 -0.302 1.00 0.00 H ATOM 51 HA GLN 4 6.102 2.559 -2.329 1.00 0.00 H ATOM 52 2HB GLN 4 5.767 3.012 0.708 1.00 0.00 H ATOM 53 3HB GLN 4 4.513 3.282 -0.501 1.00 0.00 H ATOM 54 2HG GLN 4 5.914 5.145 -1.550 1.00 0.00 H ATOM 55 3HG GLN 4 7.170 4.884 -0.366 1.00 0.00 H ATOM 56 1HE2 GLN 4 4.318 6.315 1.939 1.00 0.00 H ATOM 57 2HE2 GLN 4 4.391 4.557 1.374 1.00 0.00 H ATOM 58 N NME 5 8.549 3.501 -1.271 1.00 0.00 N
Re: [gmx-users] (no subject)
- Original Message - From: munu...@yahoo.com Date: Monday, June 28, 2010 5:29 Subject: [gmx-users] (no subject) To: gmx-users@gromacs.org --- | Hellow, My sequence was processed with SPDBV which add NH3 and COO- at the Nterminal and Cterminal respectively thereby MD simulation was carried out using GROMACS versions of 3.3.2 and 4.0. The system was working well. Now I would like to add protecting groups i.e.acetyl group (CH3CO) and Nmethyl (NHCH3) at the N and C terminal respectively instead of NH3 and COO- using Gromacs 4.0. Kindly suggest me needful action for the said construction. Or kindly suggest the software which can construct like CH3CO-Gly-trp-lys- - - - - - - - NHCH3 thereby getting output file can be used by GROMACS 4.o for completing my MD of the molecuel having such a sequence any like CH3CO-Gly-trp-lys- - - - - - - - NHCH3 . | --- You will need some non-GROMACS software to do this. Some suggestions are here http://www.gromacs.org/Documentation/File_Formats/Coordinate_File 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/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/mailing_lists/users.php
Re: [gmx-users] (no subject)
Amin Arabbagheri wrote: Hi all, I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package manager. I want to run a simulation in parallel on a multi processor, single PC, but to compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, it still runs as a single job. Thanks a lot for any instruction. Regarding grompp: http://www.gromacs.org/Documentation/FAQs As for mdrun, please provide your actual command line. The mdrun -np flag is nonfunctional, instead the number of nodes are taken from, i.e. mpirun -np from which mdrun is launched. -Justin Bests, Amin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
