[gmx-users] (no subject)
sir, I have a basic doubt about remd simulation. In remd is it possible to run 16 replicas in 8 processors? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear GMX Users, I am wish to perform a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a open-state, the system moves to the closed-state and just stays there forever (20 ns) simulation. I use the following command. make_edi -f eigenvec.trr -eig eigenval.xvg -s 1pdb.pdb -o sam.edi -flood 7-16 -tau 0 -Eflnull 450.0 -hessian -alpha 2 -ori 1pdb.pdb -T 50 the eigenvec.trr was generated from anisotropic network models. How should I organize the different parameters to effect this transition. As of now I am executing my commands (and also my understanding) are based on the following paper: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20473/abstract Best, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear Gromacs users, Please somebody help . editconf computs the incorrect value of mass of input. I tried to resolve this problem but failed. Previously I was doing AOt but now I just found that the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp atomtypes.atp. The mass of input should be 15.99940 but it showing 222. Please help me whether this is bug or something wrong with my GROMACS. Its GROMACS version 5.4.5. I calculate for just 1 atom to see error I have just 1 atom in my pdb so only on in .rtp too A.pdb CRYST1 12.000 12.000 12.000 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 OS1 AOT 151 7.820 -5.791 -0.815 1.00 0.00 O ENDMDL TER RM.rtp [AOT ] ; [ atoms ] OS1 O2L -0.6000 1 [ bonds ] atomtypes.atp NTL 14.007000 ; ammonium nitrogen NH3L 14.007000 ; nitrogen phosphatidylethanolamine OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) OCL 15.999400 ; acetate oxygen OSL 15.999400 ; ester oxygen OSLP 15.999400 ; Phosphate oxygen, to avoid conflict with methylacetate type O O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate OHL 15.999400 ; Nucleic acid phosphate hydroxyl oxygen PL 30.974000 ; phosphorus SL 32.06 ; Sulfate sulfur SOD 22.989770 ; Sodium Ion MG 24.305000 ; Magnesium Ion OUTPUT OF editconf Volume of input 125 (nm^3) Mass of input 222.295 (a.m.u.) This is incorrect, even to much incorrect. It should be 15.40 Density of input 2.95304 (g/l) Scaling all box vectors by 0.143468 new system size : 0.000 0.000 0.000 shift : 2.141 2.141 2.141 (nm) new center : 2.500 2.500 2.500 (nm) new box vectors : 5.000 5.000 5.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 125.00 (nm^3) Many Many Thanks for your help Hari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Hi, Please tell me what is wrong in my input file. I am not getting APL along with std deviation values. Following is the input and output for calculating APL Input file coord_file md.gro file_type gro num_frames1 num_lipid_types 1 resname1 POPC atomname1 P8 solvent SOL ions CL- ## Define the size and shape of the grid box_sizevectors grid200 conserve_ratio yes ## Define whether there is a protein embedded in the bilayer protein yes precision 1.3 P_value 6.0 ## Define the desired output files and format output_prefix output output_format column thickness no areayes Output: Reading from PC_APL... You defined the coordinate file as md.gro You specified that this file contains 1 frame(s) You defined a lipid residue name as POPC (atom(s): P8) You defined the solvent as SOL You defined the ions as CL- Deconstructing lipid bilayer... Lower X limit: 0.4365999 Upper X limit: 6.696 Lower Y limit: 0.2762 Upper Y limit: 6.476 Cross sectional area (box size) was determined from: a line in the coord file Cross sectional area of the system: 6.25940 x 6.19980 nanometers Lower Z limit: -0.328 Upper Z limit: 5.269 The middle (in the Z-direction) is 2.4705 In the top leaflet, the Z values range from 4.223 to 5.269 In the bottom leaflet, the Z values range from -0.328 to 1.616 Simulating periodic boundary conditions...Done Dividing the periodic array into a top and bottom leaflet...Done Looking for offending protein atoms... There are 10 protein atoms within the headgroups of the top leaflet There are 18 protein atoms within the headgroups of the bottom leaflet Simulating periodic boundary conditions for the protein atoms...Done Dividing the periodic array into a top and bottom leaflet...Done Generating the grid... Your system is bigger in the X-direction There are 200 grid points in the X direction, spaced every 0.03145 nanometers There are 198 grid points in the Y direction, spaced every 0.03147 nanometers Note: the intervals may not be exactly the same in order to have a whole number of grid points Analyzing the bilayer... Calculating area per lipid head group... The lateral area of the system is 3880.70281 sq. Angstroms (per side) When you don't account for any protein atoms: The average area per lipid in the top leaflet is 61.59846 sq. Angstroms The average area per lipid in the bottom leaflet is 59.70312 sq. Angstroms When you do take the protein atoms into account: The new area per lipid in the top leaflet is 60.66670 sq. Angstroms The new area per lipid in the bottom leaflet is 54.70072 sq. Angstroms The top leaflet lipid areas will be printed to output.frame1.200x198.top_areas.d at The bottom leaflet lipid areas will be printed to output.frame1.200x198.bottom_a reas.dat -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear gmx-users, We intend to perform free energy calculations by pulling a polypeptide along water-hexane interface. We need to pull the polypypeptide from the water layer towards the hexane layer (crossing the interface). For this we position restrained one hexane molecule in the bulk of hexane (pull_group0) and trying to pull the polypeptide (pull_group1) towards it. But though the polypeptide is getting pulled, the hexane layer is breaking in the process. The pulling options used are as follows, pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N Y N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = 3 pull_group1 = Protein pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 We have also played a bit with the pull rate and pull constant, but same thing happens. Are we doing something wrong? Can you please help? -- Prithvi Raj Pandey National Chemical Laboratory, Pune 411008. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
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. Thanks -- 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 9/30/13 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
[gmx-users] (no subject)
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. maryam abbasi, PhD student of Medicinal Chemistry Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences (http;//pharm.mui.ac.ir/) Isfahan University of Medical Sciences (http://www.mui.ac.ir), Hezar Jerib Ave. Isfahan, I.R.IRAN -- 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
[gmx-users] (no subject)
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, Awaiting For your reply Thanking You -- 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
[gmx-users] (no subject)
In an implicit, non-periodic system, it is more likely that the ligand will float away from the protein. I've tried it and that's all that ever happens. Moreover, the current Gromacs version does not support implicit solvent on GPU and the previous version that did had very limited functionality. -Justin Hm, I am probably completely wrong about this, but can you do implicit solvent and Periodic Box Conditions? If so, does it give similar ns/day? Thanks! -- 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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hi please help me must all mdp files to be similar for g_lie program? shouldn't i use of PME in all mdp files? what edr file must i use as input file for g_lie? best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
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 Thanks for your help -- 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
[gmx-users] (no subject)
http://1515-org.com/njpczvkv/uvjeyddwjvclsn.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
On 2013-06-01 02:24, Marcelo Vanean wrote: Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear Sir, In pulling simulations how to set pull_rate and pull_k .On which basis we can set these values. -- 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] (no subject)
Dear all.I want to study Diffusion coefficient of carbonmonoxide in water...I get different values of force constant partial charge while searching for those constants. Can anyone help me providing the values of partial charge (of CO), force constant and lennard jones parameter used in the simulation processThanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials for calculating youngs modules ,stress and strain. Thank You -- 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] (no subject)
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] (no subject)
I want to do simulation of protein at pH 12, in this case experimentally reported that the disulphide bonds of protein was broken and sulphurs become S negative . Can you please tell me making of disulphide as S- and S- is it correct and how to set force field to this. Thank you. -- 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
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
[gmx-users] (no subject)
I want to do simulation of protein at pH 12 so i have to deprotanate tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx command -- 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] (no subject)
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? Thanks alot. S. Faraji -- 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
[gmx-users] (no subject)
Dear All I have done the lysozyme tutorial and at the end of the simulation a .gro file have been produced. would you please tell me whether this gro file contains the structure of our molecules at the end of simulation or not? I mean does it show the simulation box at the end of simulation? regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Hai I have done 10ns simulation for a protein to this i want to calculate DCCM map.can you please suggest me how to calculate this map. Thank You. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
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
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
[gmx-users] (no subject)
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? I use this file for PR step , but I get this error: 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 -- 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
[gmx-users] (no subject)
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. 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). Fatemeh Ramezani -- 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
[gmx-users] (no subject)
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? -- 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
[gmx-users] (no subject)
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[gmx-users] (no subject)
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[gmx-users] (no subject)
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[gmx-users] (no subject)
Hi friends, I'm interested in using Thole type model for water (polarizable) TTM2 J. Phys. Chem. A, 2006, 110 (11), pp 4100 or TTM3 ;J. Chem. Phys. 128, 074506 (2008) ) model. Can someone send me itp file for water.. Thanks Ananya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear all,
When I try to install gromacs-4.5.5 on my centos system, I meet trouble. I
installed fftw-3.3.2 and then install gromacs-4.5.5. When I type /.configure
command, I got the error information:
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name...
configure: error: in `/gromacs/gromacs-4.5.5':
configure: error: C compiler cannot create executables
See `config.log' for more details.
The content of the config.log is the as following:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by gromacs configure 4.5.5, which was
generated by GNU Autoconf 2.64. Invocation command line was
$ ./configure --disable-float --prefix=/gromacs/gromacs-4.5.5
## - ##
## Platform. ##
## - ##
hostname = localhost.localdomain
uname -m = i686
uname -r = 2.6.18-308.el5
uname -s = Linux
uname -v = #1 SMP Tue Feb 21 20:05:41 EST 2012
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = i686
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/kerberos/sbin
PATH: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/X11R6/bin
PATH: /home/sunyp/bin
## --- ##
## Core tests. ##
## --- ##
configure:3028: checking build system type
configure:3042: result: i686-pc-linux-gnu
configure:3062: checking host system type
configure:3075: result: i686-pc-linux-gnu
configure:3112: checking for a BSD-compatible install
configure:3180: result: /usr/bin/install -c
configure:3191: checking whether build environment is sane
configure:3241: result: yes
configure:3382: checking for a thread-safe mkdir -p
configure:3421: result: /bin/mkdir -p
configure:3434: checking for gawk
configure:3450: found /usr/bin/gawk
configure:3461: result: gawk
configure:3472: checking whether make sets $(MAKE)
configure:3494: result: yes
configure:3569: checking how to create a ustar tar archive
configure:3582: tar --version
tar (GNU tar) 1.15.1
configure:3585: $? = 0
configure:3625: tardir=conftest.dir eval tar --format=ustar -chf - $tardir
conftest.tar
configure:3628: $? = 0
configure:3632: tar -xf - conftest.tar
configure:3635: $? = 0
configure:3648: result: gnutar
configure:4308: checking for cc
configure:4324: found /usr/bin/cc
configure:4335: result: cc
configure:4366: checking for C compiler version
configure:4375: cc --version 5
cc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-52)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:4386: $? = 0
configure:4375: cc -v 5
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk
--disable-dssi --disable-plugin
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic
--host=i386-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-52)
configure:4386: $? = 0
configure:4375: cc -V 5
cc: '-V' option must have argument
configure:4386: $? = 1
configure:4375: cc -qversion 5
cc: unrecognized option '-qversion'
cc: no input files
configure:4386: $? = 1
configure:4408: checking for C compiler default output file name
configure:4430: cc /gromacs/fftw-3.3.2/include conftest.c 5
/gromacs/fftw-3.3.2/include: file not recognized: Is a directory
collect2: ld returned 1 exit status
configure:4434: $? = 1
configure:4471: result:
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.5.5
| #define PACKAGE_STRING gromacs 4.5.5
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE_URL
| #define PACKAGE gromacs
| #define VERSION 4.5.5
| #define GMX_DOUBLE /**/
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Mon Oct 8 18:32:11 PDT 2012
| #define BUILD_USER root@localhost.localdomain
| #define BUILD_MACHINE Linux 2.6.18-308.el5 i686
| /* end confdefs.h. */
| #include stdio.h
| int
| main ()
| {
| FILE *f = fopen
[gmx-users] (no subject)
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear Gromacs users, I would like to simulate water on Ruthenium surface. Would you please suggest the force field used to describe Ru. Many thanks. -- 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 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
[gmx-users] (no subject)
Dear gmx users I am analyzing simulation results of a system including carbon nanotube+surfactant molecules. I would like to calculate the number of surfactants located on a specific distance(say 1 nm ) from nanotube in each timestep or average of that quantity.I would be really appreciated if someone could help to calculate that?is there any program in gromacs to do that? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
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. Lingyun -- 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 8/28/12 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
[gmx-users] (no subject)
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. #!/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 -- 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 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
[gmx-users] (no subject)
Dear gmx-users I am trying to calculate the optical rotation of a molecule in solution. There are several examples of this in the literature where they take snapshots of molecule at intervals throughout the trajectory, calculate optical rotation, and average them to get a solvated optical rotation. I have tried using this method by my numbers don't seem to converge on any one value, for example over 6ns trajectory, using 3000 snapshots I get a calculated rotatory power of ~20 deg/cm average with a standard deviation 745 deg/cm! (calculated with atom-dipole interaction model). my molecule does have a long carbon chain which may be the problem. So would it help to pick out the most common configurations and do calculations on them perhaps? is there a feature of gromacs that will determine the most probable conformations? Also I set up an single point energy calculation of each snapshot using mdrun -rerun (but this is on the unsolvated molecule) for possible comparison of the snapshot energies, but is there a better way of getting these energies from the energy file? Thanks in advance for any responses Cody Covington -- 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] (no subject)
Dear Sir, Thanks sir. I am using the ffG43a1 force field. Mine is an unusual unusual peptide and got the necessary files from prodrg server. and also pasting the top file. Please tell where , m making the mistake. The Force Fields to be included #include ffG43a1.itp ; Include nmab2 topology #include nmab2.itp ; Include water topology #include spc.itp ; Include position restraint file #ifdef POSRES #include posre.itp #endif #ifdef POSRE_WATER ; Position Restraint for each water oxygen [ position_restraints ] ; i functfcx fcyfcz 1 1 1000 1000 1000 #endif [ system ] ; Name DRG in water [ molecules ] ; Compound#mols DRG 1 SOL 397 Thanks Sir. Radhika -- 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] (no subject)
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. I tried to registration again, but in the section Type the characters you see in the image below , it isn't shown anything!!! Please help me. Thank you very much in advance. Best Regards Sara -- 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 7/14/12 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
[gmx-users] (no subject)
g_energy -dp IIRC. g_energy -h is your friend. By the way in single precision you have 7-8 digits only. It seems that the X.edr file only contains 6 digits (if mdrun was done with single precision). So g_energy -f X.edr -dp gives me only 6 digits. To wish list: X.edr file should contain as many digits as possible. Terveisin, Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: Karjaan lukio --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068 -- 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] (no subject)
Dear Gromacs Users, I have a system consists of cyclohexan, pentanol, surfactant and water in MARTINI coarse-grained ff, when I do pr.mdp for this system (posre.itp file is only for surfactant), water molecules are not distributed and are aggregated in one place in the box. I don't know what should I do! Can you help me, Please? Thanks in advance. Best Regards Sara -- 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] (no subject)
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? Regards, Amir -- 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 6:00 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
Re: [gmx-users] (no subject)
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
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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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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?? -- 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 6/19/12 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
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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. please help!! -- 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 6/18/12 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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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. Suryanarayana Seera, JRF, India. -- 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
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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
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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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how to assign charge and charge group number when new residue as being added to the existing amino acid rtp file -- 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
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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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http://livehistorytours.com/wp-content/uploads/wapple-architect/images/postHeader/loveit.php?public138.jpg-- 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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pa href=http://tgiturkiye.net/breakingnews/63LeePhillips/;http://tgiturkiye.net/breakingnews/63LeePhillips//a/p -- 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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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 .. Thank you in advance .. With Best Wishes, Rama David -- 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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Dear Justin I really appreciate for your reply. -- 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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Hi Guys I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP based charges for some molecules that I study using OPLSAA force field. Is this a correct method to do so if not please let me know what are the other methods that are available. thanks alot Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA-- 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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Hello, I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I am running simulation for 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 For second case I am using rerun option to calculate the energy with charge for same configuration. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o md-rerun.tpr /opt/mpich_intel/ch-p4/bin/mpirun -machinefile cp -np 2 /usr/local/gromacs/bin/mdrun_mpi -s md-rerun.tpr -o md-rerun.trr -c solvent-bmi-pf6-128.pdb -e md-rerun.edr -rerun md.trr -g md-rerun.log The total energy difference between change and neutal is large around ~350 kj/mole. It should be around 30 kJ /mole. Can you tell why I getting large high energy differmece. I using Gromacs VERSION 4.0.5. NIlesh -- 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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Rev0Iuti0n - h0me business http://transcom68.com/httpckhatcpa12k2.php?pesIDid=318 Wed, 4 Apr 2012 4:31:32 __ Peter Wilks lives? they givea glance at one another, and nodded their heads, as much as to say, Whatd I tell you? Then one of them says, kind of soft and gentle:Im sorry sir, but the best we can do is to tell you where he DID liveyesterday evening. (c) connie willaburh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear Gromacs users,
I am performing MD simulation of an 14 units oligosaccharide on Gromacs
4.5.4. I am able to successfully do a 10 ns simulation on a DELL-precision
workstation and also a 5ns simulation on tyrone cluster using a PBS script
(shown below). However, when I am trying to proceed for further consecutive
5ns simulation, I get an error saying no domain decompositions error. I
have tried changing the number of nodes by making it to 16 but it showed
the same error. whereas, when I tried it on the same workstation as before,
the mdrun has successfully executed. Please help me in letting me know what
is the problem with the system and what parameters or argument I am missing
while running it in tyrone cluster. I am providing the md.mdp parameter and
the PBS script are also provided as attachments to this mail
*
**the error is:*
Program mdrun_mpi_d, VERSION 4.5.4
Source code file: domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 32 nodes that is compatible with the
given box and a minimum cell size of 1.33444 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
*and the PBS script is as below:*
#!/bin/sh
#PBS -N test
#PBS -l nodes=1:ppn=32:debug
#PBS -l walltime=2:00:00
#PBS -S /bin/sh
#PBS -j oe
curr_dir=${PBS_O_WORKDIR}
cd ${PBS_O_WORKDIR}
NPROCS='wc -l $PBC_NODEFILE'
HOSTS='cat $PBS_NODEFILE | uniq |tr '\n' '
echo Running Directory is 'pwd'
/opt/mvapich2-1.7rc1/gcc/bin/mpirun -np 32
/home/proj/11/mbumasha/programs/gromacs-4.5.4/bin/mdrun_mpi_d -deffnm
triglc-MD4 -c triglc-MD6.pdb
*Please suggest me how to resolve this error.
*
Thank you in advance.
Dr. M. Asha Latha Sreshty,
PDF,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore,
INDIA
test.o4101
Description: Binary data
md.mdp
Description: Binary data
test3.sh
Description: Bourne shell script
--
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[gmx-users] (no subject)
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. 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? Thanking in advance. Anik Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- 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)
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
[gmx-users] (no subject)
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 -- 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
[gmx-users] (no subject)
Dear Gromacs users! I want to simulate membrane receptor in the Gromos 56 force field in the vacuu and I have some methodological questions. 1- I need to edit topology of my structure by adding one DOUBLE covalent bond between desires atoms ( they have been already placed in the desired adjacent positions by pymol). I add string in topology.top [bonds] 2809 2810 2gb_5 Does it enough? What addition modification of the topology file requires for the addition covalent bond? Where I could found names of all bonds parametrs such as gb_5 ? I've found that number for the C=O pair so as I understood this must correspond to double planar bond. 2- I've received message that my system consist of 2 negative charges. For water-souluble proteins I just place 2 counter ions in the SOLVENT to neitralize this charge. What I should do for the vacuu simulation ? Thanks! James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
The following is a part of the dna pdb file, which I am using: ATOM 1 OH DG5 X 1 13.663 36.760 21.465 0.00 0.00 ATOM 2 CT DG5 X 1 14.791 36.040 21.150 0.00 0.00 ATOM 3 CT DG5 X 1 14.771 34.703 21.873 0.00 0.00 ATOM 4 OS DG5 X 1 16.017 34.553 22.577 0.00 0.00 ATOM 5 CT DG5 X 1 13.724 34.528 22.970 0.00 0.00 ATOM 6 OS DG5 X 1 13.540 33.118 23.234 0.00 0.00 I am using amber 03 forcefield (amber03.ff) whose atom type is as follows: H0 1.00800 ; H aliph. bond. to C with 1 electrwd. group (03GLY) Br79.9; bromine C 12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction CC12.01000; sp2 aromatic C, 5 memb. ring HIS CK12.01000; sp2 C 5 memb.ring in purines CM12.01000; sp2 C pyrimidines in pos. 5 6 .. The dna-rtp file in the amber 03 is as follows: [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove impropers over the same bond as a proper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 9 41 3 1 0 ; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's [ DA5 ] [ atoms ] H5THO0.44220 1 O5'OH -0.63180 2 C5'CT -0.00690 3 H5'1H10.07540 4 [ DG5 ] [ atoms ] H5THO0.44220 1 O5'OH -0.63180 2 C5'CT -0.00690 3 H5'1H10.07540 4 H5'2H10.07540 5 C4'CT0.16290 6 H4'H10.11760 7 O4'OS -0.36910 8 C1'CT0.03580 9 ... But then also when I am running the file with the command: pdb2gmx -f dna5.pdb -o dnA5.pdb -p topol.top with TIP3P water model I am getting the following error: Identified residue DG51 as a starting terminus. Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA). Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA). Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA). Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA). Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue DG51 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn --- Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OH in residue DG5 1 was not found in rtp entry DG5 with 31 atoms while sorting atoms. Anik Sen Student CSIR-Central Salt Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Hello, I am trying to a simple energy minimization with my DNA molecule I created with 3DNA program. Below is a snippet of a pdb file where I've only included coordinates for one residue to save space (Actual file contains coordinates for 12-mer DNA). So my question is why is the pdb2gmx spitting out Fatal Error: Atom P in residue DG 0 not found in rtp entry entry DGN with 32 atoms while sorting atoms? I am using forcefield94 and looking at the .rtp file and atom P is surely present in the forcefield. Is the pdb format? Something else? If it the format then does anyone know how to properly put together a pdb file of a nucleic acid and show me what it looks like, and what forcefields are good for DNA ligand interactions? thanks in advance REMARK3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab. ATOM 1 P DG A 1 -0.356 9.218 1.848 ATOM 2 O1P DG A 1 -0.311 10.489 2.605 ATOM 3 O2P DG A 1 -1.334 9.156 0.740 ATOM 4 O5' DG A 1 1.105 8.869 1.295 ATOM 5 C5' DG A 1 2.021 8.156 2.146 ATOM 6 C4' DG A 1 2.726 7.072 1.355 ATOM 7 O4' DG A 1 1.986 5.817 1.352 ATOM 8 C3' DG A 1 2.952 7.370 -0.127 ATOM 9 O3' DG A 1 4.210 6.832 -0.518 ATOM 10 C2' DG A 1 1.848 6.598 -0.850 ATOM 11 C1' DG A 1 1.913 5.344 0.016 ATOM 12 N9DG A 1 0.711 4.472 -0.101 ATOM 13 C8DG A 1 -0.606 4.826 -0.294 ATOM 14 N7DG A 1 -1.430 3.807 -0.354 ATOM 15 C5DG A 1 -0.599 2.700 -0.190 ATOM 16 C6DG A 1 -0.914 1.317 -0.165 ATOM 17 O6DG A 1 -2.010 0.775 -0.284 ATOM 18 N1DG A 1 0.233 0.533 0.025 ATOM 19 C2DG A 1 1.516 1.023 0.172 ATOM 20 N2DG A 1 2.476 0.111 0.344 ATOM 21 N3DG A 1 1.811 2.321 0.149 ATOM 22 C4DG A 1 0.709 3.095 -0.035 END-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Hi all, I am new to the Gromacs and just started to use Gromacs for MD simulations. I am tring to extend the simulation (protein in a box) 10 ns more. For this, I used the following command: grompp -f md.mdp -c md_first.gro -t md_first.cpt -p topol.top -o md_second.tpr mdrun It seems to run.. I am just wondering am I right or should I also use the tpbconv as it is stated in the http://www.gromacs.org/Documentation/How-tos/Extending_Simulations. Thanks, Turgay -- 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
