[gmx-users] Extracting .gro file from a crashed run
Hello dear users, I was running a simulation which crashed (without writing output.gro file) Is there a way to extract the .gro file somehow from .trr or any other file? Please guide. Thanks, SN -- 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] to find out number of solvent molecules within certain radius of the protein
Hi, Where can I find the documentation for g_select? Thanks, SN On Tue, Jul 26, 2011 at 6:07 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Dear gmx-users, >> >> I wish to calculate the number of solvent molecules within certain radius >> of the protein all through the trajectory. >> >> Is there any utility available with gromacs to do so? >> >> > Dynamic selections can be made with g_select. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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] to find out number of solvent molecules within certain radius of the protein
Dear gmx-users, I wish to calculate the number of solvent molecules within certain radius of the protein all through the trajectory. Is there any utility available with gromacs to do so? Thanks, SN -- 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] genbox -shell
Hi All, I have a question about genbox -shell option. The online manual says: *-shell* real 0 thickness of optional water layer around solute The value specified for -shell option, example 3, produces a sphere with radius 3 nm or diameter 3 nm? Thanks, SN -- 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] branched polyhistidine chain
Hi gmx-users, Is there a way to create a branched polyhistidine chain using gromacs, instead of a straight chain? Thanks, SN -- 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] mpirun and no pbc
Dear gmx-users, I am heating my system at 300 K. I have set the pbc conditions as "no" I get the following error: --- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 5436 Fatal error: pbc type no is not supported with domain decomposition, use particle decomposition: mdrun -pd --- I tried looking for a similar option as "-pd" for parallel runs, but could not find any. The md.mdp is: ; Run parameters integrator = md ; leap-frog integrator nsteps = 50 ; 2 * 50 = 1000 ps, 1 ns dt= 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = simple ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics ;coulombtype = PME; Particle Mesh Ewald for long-range electrostatics ;pme_order = 4 ; cubic interpolation ;fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 400400 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = no pcoupltype = isotropic ; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = no; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ;comm_mode comm_mode = ANGULAR Kindly guide regarding this. Thanks, SN -- 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] building a new molecule which does not exist in gmx data base
Dear Justin and other gmx-users, As per the journal article, Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies, PRODRG 2.5 server does not assign charges compatible with GROMOS force field. PRODRG 2.5, however, assigns the correct atom types and bonded parameters. I have to build 2,5-dihydroxybenzoic acid Starting from PRODRG 2.5 produced .itp and further rectification is a good idea? If yes, what should be strategy? And if PRODRG should not be my starting point at all, then how should I go about building the molecule/anion. Please guide, as I am not well versed with gromacs. Thanks, SN -- 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] Regarding g_dist -dist option
On Fri, Jun 24, 2011 at 10:45 AM, bipin singh wrote: > Hello, > I just want to ask that in g_dist module, -dist option expect distance as a > real argument, so the distance should be in nm or A for that... > -nanometer (nm) > > -- > --- > *Regards,* > Bipin Singh > > > -- > 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] Reducing density using -vdwd option for a new solvent in the system
Hello Justin and everybody, I created a system of charged polyhistdine, counter anions and just 1 DHB molecule is a box without making any change in the vdwradii.dat file. This system does not energy minimize, it stops with the same message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. What can be done to fix this problem? The part of DHB itp file is: [ moleculetype ] ; Name nrexcl DHB 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DHB OAA 1 -0.567 15.9994 2 C 1 DHB CAH 11.135 12.0110 3OM 1 DHB OAD 1 -0.568 15.9994 4 C 1 DHB CAK 2 -0.004 12.0110 5 CR1 1 DHB CAG 20.004 12.0110 6HC 1 DHB HAG 20.033 1.0080 7 C 1 DHB CAI 20.141 12.0110 8OA 1 DHB OAB 2 -0.179 15.9994 9 H 1 DHB HAB 20.005 1.0080 10 CR1 1 DHB CAE 30.000 12.0110 11HC 1 DHB HAE 30.000 1.0080 12 CR1 1 DHB CAF 30.000 12.0110 13HC 1 DHB HAF 30.000 1.0080 14 C 1 DHB CAJ 40.082 12.0110 15OA 1 DHB OAC 4 -0.113 15.9994 16 H 1 DHB HAC 40.031 1.0080 If I have the water/methanol or water:methanol in the system as the solvent, the system runs fine. Please help. Thanks, SN On Tue, Jun 14, 2011 at 3:13 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Dear Justin, >> >> I have run into another problem. >> >> I created the system by including DHB in vwdradii.dat as follows: >> >> ; Very approximate VanderWaals radii >> ; only used for drawing atoms as balls or for calculating atomic overlap. >> ; longest matches are used >> ; '???' or '*' matches any residue name >> ; 'AAA' matches any protein residue name >> ??? C 0.15 >> ??? F 0.12 >> ??? H 0.04 >> ??? N 0.110 >> ??? O 0.105 >> ??? S 0.16 >> *DHB C 0.5 >> DHB H 0.5 >> DHB O 0.5* >> ; Water charge sites >> SOL MW0 >> SOL LP0 >> ; Masses for vsite construction >> GLY MN1 0 >> GLY MN2 0 >> ALA MCB1 0 >> ALA MCB2 0 >> VAL MCG1 0 >> VAL MCG2 0 >> ILE MCG1 0 >> ILE MCG2 0 >> ILE MCD1 0 >> ILE MCD2 0 >> LEU MCD1 0 >> LEU MCD2 0 >> MET MCE1 0 >> MET MCE2 0 >> TRP MTRP1 0 >> TRP MTRP2 0 >> THR MCG1 0 >> THR MCG2 0 >> LYSH MNZ1 0 >> LYSH MNZ2 0 >> >> After making this change, DHB molecules were not over lapping with each >> other. >> >> I tried to energy minimized the system. >> minim.mdp >> ; minim.mdp - used as input into grompp to generate em.tpr >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> ;emtol= 1000.0; Stop minimization when the maximum force < 1000.0 >> kJ/mol/nm >> emstep = 0.01 ; Energy step size >> nsteps = 5 ; Maximum number of (minimization) steps to >> perform >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor list and long >> range forces >> ns_type = grid ; Method to determine neighbor list (simple, grid) >> rlist= 1.0; Cut-off for making neighbor list (short range forces) >> coulombtype = PME; Treatment of long range electrostatic interactions >> rcoulomb = 1.0; Short-range electrostatic cut-off >> rvdw = 1.0; Short-range Van der Waals cut-off >> pbc = xyz ; Periodic Boundary Conditions (yes/no) >> constraints = none >> >> >> After about 6000 steps the run stops with the message: >> Stepsize too small, or no change in energy. >> Converged to machine precision, >> but not to the requested precision Fmax < 10 >> >> Double precision normally gives you higher accuracy. >> >> Steepest Descents converged to machine precision in 6012 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = 1.0655116e+05 >> Maximum force = 1.6512177e+02 on atom 2076 >> Norm of force
Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system
Dear Justin, I have run into another problem. I created the system by including DHB in vwdradii.dat as follows: ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 *DHB C 0.5 DHB H 0.5 DHB O 0.5* ; Water charge sites SOL MW0 SOL LP0 ; Masses for vsite construction GLY MN1 0 GLY MN2 0 ALA MCB1 0 ALA MCB2 0 VAL MCG1 0 VAL MCG2 0 ILE MCG1 0 ILE MCG2 0 ILE MCD1 0 ILE MCD2 0 LEU MCD1 0 LEU MCD2 0 MET MCE1 0 MET MCE2 0 TRP MTRP1 0 TRP MTRP2 0 THR MCG1 0 THR MCG2 0 LYSH MNZ1 0 LYSH MNZ2 0 After making this change, DHB molecules were not over lapping with each other. I tried to energy minimized the system. minim.mdp ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) ;emtol= 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype = PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none After about 6000 steps the run stops with the message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 6012 steps, but did not reach the requested Fmax < 10. Potential Energy = 1.0655116e+05 Maximum force = 1.6512177e+02 on atom 2076 Norm of force = 6.5337501e+00 The potential energy is high, but I still continued to equilibration. After NVT equilibration, NVT equilbration runs into the following error as soon it starts: Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size /var/spool/pbs/mom_priv/jobs/1869547.lionxj.rcc.psu.edu.SC: line 14: 2359 Segmentation fault mdrun -deffnm npt So, I have three questions: 1. Is the starting structure bad? 2. Did I change the vdwd radii by a lot (0.105 to 0.5) 3. What value of table extension should be used for 1-4 interaction ( default value is?) if thats the problem to be fixed. Please guide. Thanks, SN On Tue, Jun 14, 2011 at 11:29 AM, shivangi nangia wrote: > Thanks Justin, vdwradii.dat suggestion worked :) > > > > > On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul wrote: > >> >> >> shivangi nangia wrote: >> >>> Hello dear gmx-users, >>> >>> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as >>> the solvent ( with a positively charged protein and few DHB anions) in a >>> box. >>> >>> I have created the .itp and .gro file of DHB using PRODRG. >>> >>> >> Unrelated advice - the topology is probably useless unless you've >> corrected the charges. See the paper linked from: >> >> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips >> >> >> I am able to create the system, but when I try to energy minimize the >>> system I get the message: >>> >>> Steepest Descents: >>> Tolerance (Fmax) = 1.0e+01 >>> Number of steps=5 >>> Step= 14, Dmax= 1.2e-06 nm, Epot= 9.04353e+19 Fmax= inf, atom= >>> 2781 >>> Stepsize too small, or no change in energy. >>> Converged to machine precision, >>> but not to the requested precision Fmax < 10 >>> >>> Double precision normally gives you higher accuracy. >>> >>> writing lowest energy coordinates. >>> >>> Back Off! I just backed up em.gro to ./#em.gro.1# >>> >>> Steepest Descents converged to machine precision
Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system
Thanks Justin, vdwradii.dat suggestion worked :) On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello dear gmx-users, >> >> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as >> the solvent ( with a positively charged protein and few DHB anions) in a >> box. >> >> I have created the .itp and .gro file of DHB using PRODRG. >> >> > Unrelated advice - the topology is probably useless unless you've corrected > the charges. See the paper linked from: > > http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips > > > I am able to create the system, but when I try to energy minimize the >> system I get the message: >> >> Steepest Descents: >> Tolerance (Fmax) = 1.0e+01 >> Number of steps=5 >> Step= 14, Dmax= 1.2e-06 nm, Epot= 9.04353e+19 Fmax= inf, atom= >> 2781 >> Stepsize too small, or no change in energy. >> Converged to machine precision, >> but not to the requested precision Fmax < 10 >> >> Double precision normally gives you higher accuracy. >> >> writing lowest energy coordinates. >> >> Back Off! I just backed up em.gro to ./#em.gro.1# >> >> Steepest Descents converged to machine precision in 15 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = 9.0435262e+19 >> Maximum force =inf on atom 2781 >> Norm of force =inf >> >> >> The reason behind this was that DHB molecules were on top of each other, >> highly dense system ( viewed in VMD) >> So, to reduce the density of DHB molecules, I tried using-vdwd option of >> genbox (changed from default value of 0.105 to 0.5) >> But, I got almost same number of DHB molecules using genbox. >> >> > The -vdwd option has no effect unless you're using atom names that are not > found in vdwradii.dat (see the genbox help description). Your DHB molecule > should be unaffected by the use of -vdwd. > > > >> What is the best solution to this problem as I understand, reducing the >> density of DHB molecules around the protein as a solvent or there is some >> other problem? >> >> > You need to generate a configuration in which molecules aren't overlapping. > There are several ways to accomplish this. You can manually place molecules > within a box at a desired location with editconf -center, otherwise genbox > -ci -nmol. If the locations of the molecules are not what you desire with > genbox, change the value of -seed and try again. > > -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 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] Reducing density using -vdwd option for a new solvent in the system
Hello dear gmx-users, I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as the solvent ( with a positively charged protein and few DHB anions) in a box. I have created the .itp and .gro file of DHB using PRODRG. I am able to create the system, but when I try to energy minimize the system I get the message: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 9.04353e+19 Fmax= inf, atom= 2781 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = 9.0435262e+19 Maximum force =inf on atom 2781 Norm of force =inf The reason behind this was that DHB molecules were on top of each other, highly dense system ( viewed in VMD) So, to reduce the density of DHB molecules, I tried using-vdwd option of genbox (changed from default value of 0.105 to 0.5) But, I got almost same number of DHB molecules using genbox. What is the best solution to this problem as I understand, reducing the density of DHB molecules around the protein as a solvent or there is some other problem? Thanks in advance, SN -- 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] Solvating dodecahedron
Hello All, I am trying to solvate a protein sitting in a dodecahedron using genbox. It gets solvated but a box of solvent is created around the protein. I want the protein to be sitting in a dodecahedron filed with solvent. I used the following commands: editconf -f onlyhis.gro -bt dodecahedron -box 9 -d 1 -o dodec.gro genbox -cp dodec.gro -cs mix.gro -o solv.gro I have never used this utility of creating a docecahedron nor I could find a way to view the dodecahedron shae in VMD. Am I going wrong? Thanks, SN -- 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] Fatal error: Not enough memory. Failed to realloc
Dear gmx-users, I was carrying out a continuation of an NPT equilibration from NVT. As soon the job started it ran into the following error: Fatal error: Not enough memory. Failed to realloc 1488624 bytes for nl->shift, nl->shift=0x0 (called from file ns.c, line 101) What is the error about? I did search few archives, in one someone had suggested to use an upgraded version. I am currently using 4.0.5 Is upgrading the solution to this problem? Thanks in advance, SN -- 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] sphere around a protein
Hi, Please correct me if I am wrong. In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box. When I add then the 1 Li cation, water methanol sphere, how is it necessary it will cover/solvate all the ions that I had added in the box? Some might still be in open space of the box? Thanks, SN On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul wrote: > > > Justin A. Lemkul wrote: > >> >> >> shivangi nangia wrote: >> >>> Hi Justin, >>> >>> Thanks a lot! >>> Things worked. >>> >>> Now I, however, have a different problem in extension to what I am doing. >>> >>> I was able to created a sphere of water and methanol around a polypeptide >>> and 1 Li+ ion. >>> >>> editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro >>> genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro >>> genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro >>> editconf -f his20.gro -d 0 -o onlyhis.gro >>> editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro >>> genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro >>> >>> >>> Now I need to add few more Li ions and anions in the sphere. >>> >>> I tried doing that, >>> genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top >>> >>> (1dhb.gro is 2,5-dihydrobenzoic acid anion) >>> >>> But, since the sphere 6sys.gro is essentially in a box, the dhb anions >>> ...some got randomly placed inside the sphere and some in the open spaces of >>> the box in which 6sys.gro is sitting. >>> >>> How can I place all the anions and then Li+ ions specifically inside the >>> sphere? >>> >>> >> That's what genion is for. >> > > I take that back, genion doesn't work for polyatomic ions. The better > approach is to construct your system with solute, ions (which in this case > are just other molecules floating around), etc, before adding the sphere of > solvent. > > > -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 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] sphere around a protein
Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro editconf -f his20.gro -d 0 -o onlyhis.gro editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro Now I need to add few more Li ions and anions in the sphere. I tried doing that, genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top (1dhb.gro is 2,5-dihydrobenzoic acid anion) But, since the sphere 6sys.gro is essentially in a box, the dhb anions ...some got randomly placed inside the sphere and some in the open spaces of the box in which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? Thanks a lot, SN On Wed, May 25, 2011 at 1:18 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi Justin, >> >> >> Revisiting some of the calculations I had tried to do few days back. >> >> Just as a recap I am trying to build a sphere around the protein. >> >> As you had suggested in the last messgae of this thread to make a new >> directory. I did that. >> >> I used the following commands: >> >> editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro >> genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro >> genbox -cp his1.gro -cs li_sol.gro >> >> * >> 1li.gro is:* >> 1 Li ion >> 1 >>1LI+ LI1 1.736 0.839 0.257 >> 1.86824 1.86824 1.86824 >> >> *onlyli.gro is:* >> 1 Li ion >>1 >>1LI+ LI1 7.500 7.500 7.500 >> 15.0 15.0 15.0 >> >> *mix.gro ( pre-made mix of 1:1 :: water: methanol)* >> >> li_sol.gro des look like a sphere after seeingin vmd. >> >> his1.gro is: >> UNNAMED >> 14 >>1HISH N1 0.000 0.000 0.000 >>1HISHH12 -0.033 0.000 -0.094 >>1HISHH23 -0.033 -0.082 0.047 >>1HISHCA4 0.146 0.000 0.000 >>1HISHCB5 0.204 0.120 -0.077 >>1HISHCG6 0.291 0.076 -0.190 >>1HISH ND17 0.240 0.009 -0.299 >>1HISH HD18 0.145 -0.014 -0.315 >>1HISH CD29 0.425 0.089 -0.215 >>1HISH CE1 10 0.345 -0.019 -0.382 >>1HISH NE2 11 0.458 0.027 -0.333 >>1HISH HE2 12 0.549 0.020 -0.374 >>1HISH C 13 0.195 0.000 0.146 >>1HISH O 14 0.118 0.000 0.242 >> 2.50220 0.24060 2.47531 >> >> >> >> I get the following error yet again: >> >> Fatal error: >> One of the box vectors has become shorter than twice the cut-off length or >> box_yy-|box_zy| or box_zz has become smaller than the cut-off. >> >> >> > Look at the box vectors of his1.gro - a sphere of solvent with a radius of > 6 cannot fit inside a box that is 2.5 x 0.2 x 2.5 nm^3. > > -Justin > > -- >> >> Thanks a lot in advance. >> >> Sorry about reviving few days old thread. >> >> >> Thanks, >> SN >> >> >> >> >> On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>shivangi nangia wrote: >> >>Hi Justin, >> >>I used 15 nm cubic box and 6 nm shell. >>I again tried to insert only 1 histidine molecule in the sphere. >>I get the same error >> >>Fatal error: >>One of the box vectors has become shorter than twice the cut-off >>length or box_yy-|box_zy| or box_zz has become smaller than the >>cut-off. >> >> >> >>Please provide the exact command that gives the error. I cannot >>reproduce this using a shell value less than half a box vector. You >>may also want to try starting from a clean directory - get rid of >>old files and intermediates so you're sure you're using the right >> files. >> >>-Justin >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>
Re: [gmx-users] sphere around a protein
Hi Justin, Revisiting some of the calculations I had tried to do few days back. Just as a recap I am trying to build a sphere around the protein. As you had suggested in the last messgae of this thread to make a new directory. I did that. I used the following commands: editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro genbox -cp his1.gro -cs li_sol.gro * 1li.gro is:* 1 Li ion 1 1LI+ LI1 1.736 0.839 0.257 1.86824 1.86824 1.86824 *onlyli.gro is:* 1 Li ion 1 1LI+ LI1 7.500 7.500 7.500 15.0 15.0 15.0 *mix.gro ( pre-made mix of 1:1 :: water: methanol)* li_sol.gro des look like a sphere after seeingin vmd. his1.gro is: UNNAMED 14 1HISH N1 0.000 0.000 0.000 1HISHH12 -0.033 0.000 -0.094 1HISHH23 -0.033 -0.082 0.047 1HISHCA4 0.146 0.000 0.000 1HISHCB5 0.204 0.120 -0.077 1HISHCG6 0.291 0.076 -0.190 1HISH ND17 0.240 0.009 -0.299 1HISH HD18 0.145 -0.014 -0.315 1HISH CD29 0.425 0.089 -0.215 1HISH CE1 10 0.345 -0.019 -0.382 1HISH NE2 11 0.458 0.027 -0.333 1HISH HE2 12 0.549 0.020 -0.374 1HISH C 13 0.195 0.000 0.146 1HISH O 14 0.118 0.000 0.242 2.50220 0.24060 2.47531 I get the following error yet again: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. -- Thanks a lot in advance. Sorry about reviving few days old thread. Thanks, SN On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi Justin, >> >> I used 15 nm cubic box and 6 nm shell. >> I again tried to insert only 1 histidine molecule in the sphere. I get the >> same error >> >> Fatal error: >> One of the box vectors has become shorter than twice the cut-off length or >> box_yy-|box_zy| or box_zz has become smaller than the cut-off. >> >> >> > Please provide the exact command that gives the error. I cannot reproduce > this using a shell value less than half a box vector. You may also want to > try starting from a clean directory - get rid of old files and intermediates > so you're sure you're using the right files. > > -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 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] -ci option
Dear gmx users, I want to insert few ions in my system randomly. -ci option does that, but I want various "different" random configurations of the ions in my system. Using -ci option does randomly place ions but at the same coordinates each time. Is there a way to randomly generate various configurations of ions each time on using -ci? Thanks, SN -- 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] sphere around a protein
Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. On Sun, May 8, 2011 at 9:53 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Dear Justin, >> >> No. >> >> I am still preparing the system. I want the protein in the solvent sphere. >> >> >> > I see now. You're setting a 12-nm cubic box, but then using a shell of 6 > nm, which causes neighbor searching to occur throughout the entire box. The > maximum value of -shell must be less than 1/2 the shortest box vector, so > either set up a larger box, or a smaller value of -shell. > > -Justin > > >> On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>shivangi nangia wrote: >> >>Hello, >> >>Thanks Justin, I am getting somewhere but still running into >>problems. >> >>Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 >>water-methanol mixture) in 12 nm box. >> I did the following: >>editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro >>genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro >> >> >> Then, used genbox -cp protein.gro -cs sphere.gro >>with only 1 molecule of histidine I get the same error as with >>polyhistidine ( 20 ) >> >>Fatal error: >>One of the box vectors has become shorter than twice the cut-off >>length or box_yy-|box_zy| or box_zz has become smaller than the >>cut-off. >> >> >>I presume this is from mdrun? Your system is collapsing. Without >>an .mdp file, it is not possible to diagnose anything. >> >>-Justin >> >>How can I resolve this? >> >>help needed. >> >>Thanks, >>SN >> >>On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> shivangi nangia wrote: >> >> Hi Justin and other gmx-users, >> >> I want to make a sphere around a protein (5nm).with Li >>ions and >> anions. >> >> Justin, as you had suggested to use genbox -shell option, I >> tried using it but i realized that since my protein is a >> long >> tube like structure, the shell option generated a cyclinder >> around the protein. >> >> The solvent around the protein is 1:1 water-methanol >> (pre-prepared mixture n a gro file) >> >> If I try to start with a ion and solvate it with my >>solvent (1:1 >> water methanol) using -shell option, I do get a sphere >>but then >> I am unable to insert the protein in the system. >> >> >> And why not? >> >> genbox -cp protein.gro -cs sphere.gro >> >> should do exactly what you want, provided the sphere is large >>enough >> for the protein. >> >> -Justin >> >> >> Is there another feasible route to get to my desired >> configuration of the system ? >> >> Thanks in advance >> >> >> Best, >> SN >> >> >> >> >> -- >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >>231-9080 >> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >>
Re: [gmx-users] sphere around a protein
Dear Justin, No. I am still preparing the system. I want the protein in the solvent sphere. On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello, >> >> Thanks Justin, I am getting somewhere but still running into problems. >> >> Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 >> water-methanol mixture) in 12 nm box. >> I did the following: >> editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro >> genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro >> >> >>Then, used genbox -cp protein.gro -cs sphere.gro >> with only 1 molecule of histidine I get the same error as with >> polyhistidine ( 20 ) >> >> Fatal error: >> One of the box vectors has become shorter than twice the cut-off length or >> box_yy-|box_zy| or box_zz has become smaller than the cut-off. >> >> > I presume this is from mdrun? Your system is collapsing. Without an .mdp > file, it is not possible to diagnose anything. > > -Justin > > How can I resolve this? >> >> help needed. >> >> Thanks, >> SN >> >> On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>shivangi nangia wrote: >> >>Hi Justin and other gmx-users, >> >>I want to make a sphere around a protein (5nm).with Li ions and >>anions. >> >>Justin, as you had suggested to use genbox -shell option, I >>tried using it but i realized that since my protein is a long >>tube like structure, the shell option generated a cyclinder >>around the protein. >> >>The solvent around the protein is 1:1 water-methanol >>(pre-prepared mixture n a gro file) >> >>If I try to start with a ion and solvate it with my solvent (1:1 >>water methanol) using -shell option, I do get a sphere but then >>I am unable to insert the protein in the system. >> >> >>And why not? >> >>genbox -cp protein.gro -cs sphere.gro >> >>should do exactly what you want, provided the sphere is large enough >>for the protein. >> >>-Justin >> >> >>Is there another feasible route to get to my desired >>configuration of the system ? >> >>Thanks in advance >> >> >>Best, >>SN >> >> >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >>http://lists.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at >>http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] sphere around a protein
Hello, Thanks Justin, I am getting somewhere but still running into problems. Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 water-methanol mixture) in 12 nm box. I did the following: editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro Then, used genbox -cp protein.gro -cs sphere.gro with only 1 molecule of histidine I get the same error as with polyhistidine ( 20 ) Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. How can I resolve this? help needed. Thanks, SN On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi Justin and other gmx-users, >> >> I want to make a sphere around a protein (5nm).with Li ions and anions. >> >> Justin, as you had suggested to use genbox -shell option, I tried using it >> but i realized that since my protein is a long tube like structure, the >> shell option generated a cyclinder around the protein. >> >> The solvent around the protein is 1:1 water-methanol (pre-prepared mixture >> n a gro file) >> >> If I try to start with a ion and solvate it with my solvent (1:1 water >> methanol) using -shell option, I do get a sphere but then I am unable to >> insert the protein in the system. >> >> > And why not? > > genbox -cp protein.gro -cs sphere.gro > > should do exactly what you want, provided the sphere is large enough for > the protein. > > -Justin > > > Is there another feasible route to get to my desired configuration of the >> system ? >> >> Thanks in advance >> >> >> Best, >> SN >> >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] sphere around a protein
Hi Justin and other gmx-users, I want to make a sphere around a protein (5nm).with Li ions and anions. Justin, as you had suggested to use genbox -shell option, I tried using it but i realized that since my protein is a long tube like structure, the shell option generated a cyclinder around the protein. The solvent around the protein is 1:1 water-methanol (pre-prepared mixture n a gro file) If I try to start with a ion and solvate it with my solvent (1:1 water methanol) using -shell option, I do get a sphere but then I am unable to insert the protein in the system. Is there another feasible route to get to my desired configuration of the system ? Thanks in advance Best, SN -- 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] trjorder not working
Thanks Justin, that was helpful. I have a following question. Since in my system I have both methanol and water and I want to order both of them ( my eventual aim to make a sphere), is there is way to override -na option ( for water na 4, methanol 3). Is there is way that all the components of the system get ordered with respect to the protein? or I have have to play around ordering them one by one? Thanks, SN On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello, >> >> Came back to the set of calculations I was doing few days back. >> >> I have a box of water (TIP4P), methanol, protein and DHB anions. >> >> I minimized this system. >> >> Trying to use trjorder for water molecules with respect to the protein >> (eventually I want to make a sphere by ordering and getting rid of the >> molecules I do not want) >> >> In the index.ndx file i specified atom "144" (belongs to protein) >> >> so when I run >> >> trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro >> >> I pick number associated with atom "144" and SOL ( tip4p water) and I >> generate ordered.gro >> >> The sequence for SOL changes ( random), but when I use g_dist as I go down >> the ordered.gro, there is still no trend ( ascending with respect to >> protein) >> >> >> > I suspect your index file is wrong. Presumably, you have measured > distances to individual water molecules using g_dist, which would require a > custom index group for each water molecule analyzed, correct? If you use > ordered.gro, the residue numbers will indeed be scrambled based on ordering, > but the distance will correspond to the original distance, not the ordered > one. > > The solution is to use your unordered coordinate file or .tpr file to > create the index group, then perform the distance measurements. > Alternatively, use genconf to renumber ordered.gro to get sequential > residue numbers, then create whatever index file you might need from the > renumbered coordinate file. > > > >> >> >> Also, -da 0 refers to an atom OR COM of the molecule. >> using trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o >> ordered.gro and running it >> >> and choosing "1" for protein and "14" for SOL means that gromacs >> automatically understands that protein's COM is to be used to order SOL >> (tip4p, -na 4) ?? >> >> > As the documentation is written, yes. > > > If so, then tha talso generates a .gro file which produces random water >> molecules but there is again no trend. >> >> > Same problem as above, I suspect. > > -Justin > > I am very confused about using trjorder, it will be really helpful if >> someone or Mark can help me understand. >> >> Thanks a lot >> SN >> >> >> On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham >> > mark.abra...@anu.edu.au>> wrote: >> >>On 4/29/2011 11:29 AM, shivangi nangia wrote: >> >>>Hello, >>> >>>The manual explaining trjorder says: >>> >>>trjorder orders molecules according to the smallest distance to >>>atoms in a reference group or on z-coordinate (with option -z). >>>With distance ordering, it will ask for a group of reference atoms >>>and a group of molecules. For each frame of the trajectory the >>>selected molecules will be reordered according to the shortest >>>distance between atom number -da in the molecule and all the atoms >>>in the reference group. *The center of mass of the molecules can >>>be used instead of a reference atom by setting -da to 0* >>> >>>In order to arrange water molecules in accordance with the COM of >>>the polypeptide, I chose -da 0. >>> >> >>As it says above, -da refers to an atom or COM of the molecule, not >>the reference group. This could be worded better in the documentation. >> >>Be sure you're choosing the groups you think you are choosing - you >>not copying relevant parts of your terminal output into emails is >>making things difficult. >> >>Mark >> >> >>>Am I wrong? >>> >>>Thanks, >>>SN >>> >>> >>> >>> >>>On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham >>>mailto:mark.abra...@anu.edu.au>> wrote: >>> >>>On 4/29/2011 4:08 AM, shivangi nangia wrote: >>> >>>
Re: [gmx-users] trjorder not working
Hello, Came back to the set of calculations I was doing few days back. I have a box of water (TIP4P), methanol, protein and DHB anions. I minimized this system. Trying to use trjorder for water molecules with respect to the protein (eventually I want to make a sphere by ordering and getting rid of the molecules I do not want) In the index.ndx file i specified atom "144" (belongs to protein) so when I run trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro I pick number associated with atom "144" and SOL ( tip4p water) and I generate ordered.gro The sequence for SOL changes ( random), but when I use g_dist as I go down the ordered.gro, there is still no trend ( ascending with respect to protein) Also, -da 0 refers to an atom OR COM of the molecule. using trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o ordered.gro and running it and choosing "1" for protein and "14" for SOL means that gromacs automatically understands that protein's COM is to be used to order SOL (tip4p, -na 4) ?? If so, then tha talso generates a .gro file which produces random water molecules but there is again no trend. I am very confused about using trjorder, it will be really helpful if someone or Mark can help me understand. Thanks a lot SN On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham wrote: > On 4/29/2011 11:29 AM, shivangi nangia wrote: > > Hello, > > The manual explaining trjorder says: > > trjorder orders molecules according to the smallest distance to atoms in a > reference group or on z-coordinate (with option -z). With distance > ordering, it will ask for a group of reference atoms and a group of > molecules. For each frame of the trajectory the selected molecules will be > reordered according to the shortest distance between atom number -da in > the molecule and all the atoms in the reference group. *The center of mass > of the molecules can be used instead of a reference atom by setting -da to > 0* > > In order to arrange water molecules in accordance with the COM of the > polypeptide, I chose -da 0. > > > As it says above, -da refers to an atom or COM of the molecule, not the > reference group. This could be worded better in the documentation. > > Be sure you're choosing the groups you think you are choosing - you not > copying relevant parts of your terminal output into emails is making things > difficult. > > Mark > > > Am I wrong? > > Thanks, > SN > > > > > On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham wrote: > >> On 4/29/2011 4:08 AM, shivangi nangia wrote: >> >>> Hello all, >>> >>> I am trying to order the TIP4P water molecules in my system with respect >>> to the polypeptide in my system. >>> >>> The command I am using is: >>> >>> trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro >>> >>> This runs without any error and ordered.gro is generated with random >>> sequence of water molecules. >>> >>> Just to cross check I calculated the distances between one of atoms of >>> the polypeptide and oxyegn atom of different "ordered" water molecules. >>> I found, there is no ascendig trend in the distances with respect to the >>> polypeptide as a go down in the "ordered.gro" file. >>> >>> What could be going wrong? >>> >> >> -da 0 has a particular effect - is it appropriate? Did you choose the >> right groups? You could use the -nshell option to probe what trjorder thinks >> is going on. >> >> Mark >> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun Fatal error: Domain decomposition does not support simple neighbor searching
Dear gmx-users, I have a cube (8 nm) of the system containing 1:1 :: water: methanol, a polypeptide, Li ions and 2,5-dihydroxybenzoic acid anions. I am heating this system with no PBC ( evaporation). The md.mdp file is: ; Run parameters integrator = md ; leap-frog integrator nsteps = 25 ; 2 * 25 = 500 ps, 0.5 ns dt= 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching *ns_type = simple * nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics ;coulombtype = PME; Particle Mesh Ewald for long-range electrostatics ;pme_order = 4 ; cubic interpolation ;fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 500500 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = no pcoupltype = isotropic ; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions *pbc = no * ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ;comm_mode comm_mode = ANGULAR I have run this system in past without any errors, suddenly I am constantly running into the following error if I submit my job on a cluster in que *( interactive runs fine)* Fatal error: Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors With pbc = no the only grid type an be used is simple. I tried changing the size of the cube but I still face the same problem. I am unable to understand what could be going wrong suddenly. Please guide Thanks in advance, SN -- 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] trjorder not working
Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham wrote: > On 4/29/2011 4:08 AM, shivangi nangia wrote: > >> Hello all, >> >> I am trying to order the TIP4P water molecules in my system with respect >> to the polypeptide in my system. >> >> The command I am using is: >> >> trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro >> >> This runs without any error and ordered.gro is generated with random >> sequence of water molecules. >> >> Just to cross check I calculated the distances between one of atoms of the >> polypeptide and oxyegn atom of different "ordered" water molecules. >> I found, there is no ascendig trend in the distances with respect to the >> polypeptide as a go down in the "ordered.gro" file. >> >> What could be going wrong? >> > > -da 0 has a particular effect - is it appropriate? Did you choose the right > groups? You could use the -nshell option to probe what trjorder thinks is > going on. > > Mark > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to get higher precision values for g_velacc
Dear gmx users, I am using g_velacc to calculate the velocity auto correlation. The output I am getting in .xvg file is much lower precision than I require. Is there a way to get the values in higher precision? Thanks, SN -- 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] trjorder not working
Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different "ordered" water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the "ordered.gro" file. What could be going wrong? Thanks, SN -- 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] ordering components of system using trjorder
Dear gmx-users, I wish to order the components of my system with respect to the polypeptide using trjorder. I want to select my first group as the protein and the second group to be ordered is non-protein (i.e all other components in the system except polypeptide) the command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -o ordered.gro The problem is -na "int" is required, but the rest of my system contains TIP4P water, methanol, Li ions so the na is different for all non-protein components. Is there a way to override option -na and still get non-protein part of the system ordered with respect to the polypeptide (protein) Thanks, SN -- 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] Placing anion/cation at a particular distance from peptide
Dear gmx users, I need to design a starting configuration of a polypeptide with charged side chains sitting in a box of water with Cl- ions within 7 ang of its radius. I realize that in such a system like charges will essentially prefer to be as far as possible from each other, but I still need the above stated configuration. Is there an easy way to specify the distance of the anions to be added from the peptide ? Thanks, SN -- 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] mdrun segmentation fault
Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydroxybenzoic acid anions, 1:1 water: methanol (~3000 molecules of each) in 8 nm cube I had had EM of the system using steepest decent. Outcome: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 1.5354981e+19 Maximum force =inf on atom 651 Norm of force =inf *The minim.mdp *is: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.02 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype = PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none *The nvt.mdp*: title= hist NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt= 0.002 ; 2 fs ; Output control nstxout = 100; save coordinates every 0.2 ps nstvout = 100; save velocities every 0.2 ps nstenergy = 100; save energies every 0.2 ps nstlog = 100; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = none ; lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes; assign velocities from Maxwell distribution gen_temp = 300; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I tried to decrease the step size, that also runs into seg fault error. Kindly guide. Thanks, SN -- 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] mdrun segmentation fault
Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydroxybenzoic acid anions, 1:1 water: methanol (~3000 molecules of each) in 8 nm cube I had had EM of the system using steepest decent. Outcome: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 1.5354981e+19 Maximum force =inf on atom 651 Norm of force =inf *The minim.mdp *is: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol= 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.02 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype = PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none *The nvt.mdp*: title= hist NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt= 0.002 ; 2 fs ; Output control nstxout = 100; save coordinates every 0.2 ps nstvout = 100; save velocities every 0.2 ps nstenergy = 100; save energies every 0.2 ps nstlog = 100; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = none ; lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes; assign velocities from Maxwell distribution gen_temp = 300; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I tried to decrease the step size, that also runs into seg fault error. Kindly guide. Thanks, SN -- 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] NPT equilibration
Hello, I am having problems in carrying out a NPT equilibration of my system at 500 K. System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid anion. NVT equilibration gives expected results. When I load the npt.gro file in VMD, its seems as if the molecules have fragmented/vaporized. nvt.mdp: title= hist NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt= 0.002 ; 2 fs ; Output control nstxout = 100; save coordinates every 0.2 ps nstvout = 100; save velocities every 0.2 ps nstenergy = 100; save energies every 0.2 ps nstlog = 100; update log file every 0.2 ps ; Bond parameters continuation = yes; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 500500 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off If I use the same exact system and run NVT and NPT equilibration at 300 K, everything seems to be working. What could be going wrong at 500 K? Thanks, Shivangi -- 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] autocorrelation functions
Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to modify/morph the g_velacc.c program to do other autocorrelation function calculations? Thanks, Shivangi -- 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] autocorrelation functions
Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to modify/morph the g_velacc.c program to do other autocorrelation function calculations? Thanks, SN -- 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] Check for bad contacts and/or reduce the timestep.
Hello, I am sorry, I did mean 5 nm box. I did do the energy minimization but somehow overlooked the error message at that stage. Things seems to be working now. Thanks for the time. Shivangi On Tue, Mar 29, 2011 at 2:06 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello gmx-users, >> >> I have a 5 ang box with equal number of water and methanol molecules >> (1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system is >> overall +2 charged. >> >> > If your box truly is 5 A (0.5 nm), grompp should have failed based on your > cutoffs. I assume you have a 5-nm box? > > > I am trying to to do a NVT equilibration which runs into the following >> error: >> >> >> t = 0.000 ps: Water molecule starting at atom 11816 can not be settled. >> Check for bad contacts and/or reduce the timestep. >> >> > Did you do energy minimization first? If so, what was the outcome? Were > the energies and forces acceptable? What force field are you using? The > generic information about your problem can be found at: > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > -Justin > > > the nvt.mdp is: >> >> title= hist NVT equilibration >> define = -DPOSRES ; position restrain the protein >> ; Run parameters >> integrator = md ; leap-frog integrator >> nsteps = 5 ; 2 * 5 = 100 ps >> dt= 0.002; 2 fs >> ; Output control >> nstxout = 100; save coordinates every 0.2 ps >> nstvout = 100; save velocities every 0.2 ps >> nstenergy = 100; save energies every 0.2 ps >> nstlog = 100; update log file every 0.2 ps >> ; Bond parameters >> continuation = no ; first dynamics run >> constraint_algorithm = lincs ; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> ; Neighborsearching >> ns_type = grid ; search neighboring grid cells >> nstlist = 5 ; 10 fs >> rlist= 1.0; short-range neighborlist cutoff (in nm) >> rcoulomb = 1.0; short-range electrostatic cutoff (in nm) >> rvdw = 1.0; short-range van der Waals cutoff (in nm) >> ; Electrostatics >> coulombtype = PME; Particle Mesh Ewald for long-range electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.16 ; grid spacing for FFT >> ; Temperature coupling is on >> tcoupl = V-rescale ; modified Berendsen thermostat >> tc-grps = Protein Non-Protein ; two coupling groups - more accurate >> tau_t= 0.1 0.1 ; time constant, in ps >> ref_t= 250250 ; reference temperature, one for each group, in K >> ; Pressure coupling is off >> pcoupl = no ; no pressure coupling in NVT >> ; Periodic boundary conditions >> pbc = xyz; 3-D PBC >> ; Dispersion correction >> DispCorr = EnerPres ; account for cut-off vdW scheme >> ; Velocity generation >> gen_vel = yes; assign velocities from Maxwell distribution >> gen_temp = 250; temperature for Maxwell distribution >> gen_seed = -1 ; generate a random seed >> >> I did try to reduce the timestep from 2 fs to 1 fs but ran into the same >> error. >> >> >> >> Searching through a few archives I got a hint it is something do to with >> water's density per cubic nm. >> Is that whats going on here? >> If yes, then how do I randomly delete some water molecules from my system? >> >> Please help. >> >> Thanks, >> Shivangi >> >> >> >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Check for bad contacts and/or reduce the timestep.
Hello gmx-users, I have a 5 ang box with equal number of water and methanol molecules (1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system is overall +2 charged. I am trying to to do a NVT equilibration which runs into the following error: t = 0.000 ps: Water molecule starting at atom 11816 can not be settled. Check for bad contacts and/or reduce the timestep. the nvt.mdp is: title= hist NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout = 100; save coordinates every 0.2 ps nstvout = 100; save velocities every 0.2 ps nstenergy = 100; save energies every 0.2 ps nstlog = 100; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb = 1.0; short-range electrostatic cutoff (in nm) rvdw = 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 250250 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes; assign velocities from Maxwell distribution gen_temp = 250; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I did try to reduce the timestep from 2 fs to 1 fs but ran into the same error. Searching through a few archives I got a hint it is something do to with water's density per cubic nm. Is that whats going on here? If yes, then how do I randomly delete some water molecules from my system? Please help. Thanks, Shivangi -- 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] Placing ions at a required distance
Thanks, I did it manually using 'cat'. Thanks for your time. -Shivangi On Mon, Mar 28, 2011 at 4:47 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi again, >> >> I did not quite understand the suggestion. >> I have successfully added Li+ ions in my simulation box using genion. >> I am confused about how to place Li+ ions using editconf. >> >> > Are these ions simply going to be part of the bulk solution? If so, use > genion. Manual intervention is not necessary since random initial > velocities will disrupt any sort of idealized geometry that you construct. > > > Will I have to create a .gro and .itp file and add it like a solute ? >> >> > Yes and no. If you really believe you need a specific location of a Li+ > ion in your simulation cell, either (1) write a simple .gro file by hand and > concatenate it with the coordinate file of your other system components or > (2) use editconf -center to define its coordinates and concatenate that file > with your system. Li+ parameters should be present in ions.itp for most > force fields, so just #include that topology like you would any other > system. > > -Justin > > Thanks, >> Shivangi >> >> >> >> >> On Mon, Mar 28, 2011 at 3:26 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>shivangi nangia wrote: >> >>Hello, >> >>I am a new gromacs user. >> >>I want to place Li+ ions at a required distance from the >>polypeptide ( which is at the centre of a box of water) >> >>I searched through the archive and the manual if there is a >>way/provision to do this, but could not. >> >>Is there a way? >> >> >>Measure the distance you want and establish the coordinate at which >>you wish to place the ion, then use editconf -center to place it at >>the proper location in the simulation box. >> >>-Justin >> >> >> >>Please guide. >> >>Thanks, >>Shivangi >> >> >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >>http://lists.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at >>http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Placing ions at a required distance
Hi again, I did not quite understand the suggestion. I have successfully added Li+ ions in my simulation box using genion. I am confused about how to place Li+ ions using editconf. Will I have to create a .gro and .itp file and add it like a solute ? Thanks, Shivangi On Mon, Mar 28, 2011 at 3:26 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello, >> >> I am a new gromacs user. >> >> I want to place Li+ ions at a required distance from the polypeptide ( >> which is at the centre of a box of water) >> >> I searched through the archive and the manual if there is a way/provision >> to do this, but could not. >> >> Is there a way? >> > > Measure the distance you want and establish the coordinate at which you > wish to place the ion, then use editconf -center to place it at the proper > location in the simulation box. > > -Justin > > >> >> Please guide. >> >> Thanks, >> Shivangi >> >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Placing ions at a required distance
Hello, I am a new gromacs user. I want to place Li+ ions at a required distance from the polypeptide ( which is at the centre of a box of water) I searched through the archive and the manual if there is a way/provision to do this, but could not. Is there a way? Please guide. Thanks, Shivangi -- 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: Re: Re: Re: [gmx-users] Hydroixde Ion
Hi, Thanks so much for the prompt help. Yes, I did realize that methanol as solvent was not updated in the .top file. I had to fix the .top file manually. When I add ions using genion I replace methanol. As a test I tried setting up the whole system with the change that instead of 8 hydroxide ions I added 8 chloride ions. And everything works perfectly! So, I think its something with the hyrdroxide ion. I will try adding hydroxide ions using genbox. I think then I need to treat it as a charged residue and have it included in the .rtp file, correct? Thanks, Shivangi Shivangi Nangia Garrison Group Graduate Student 201A Chemistry Building University Park PA 16802 SHIVANGI NANGIA wrote: > Hi again, > > I have the following: > > I have not changed anything in ffG53a6.atp and .rtp > As suggested by gmx users, I have the following in the ions,itp file > > [ moleculetype ] > ; molname nrexcl > OH1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > 1 OH 1 OHOH 1 0 > 1 OW 1 OWOW 1 -1 > > > I executed the following commands: > > (a) pdb2gmx -f his8.pdb -ignh -ter -his -p topol.top -o his8.gro > (b) editconf -f his8.gro -box 5 5 5 -o his8box.gro > (c) genbox -cp his8box.gro -ci 1methanol.gro -nmol 1800 -o his8_meoh.gro -p topol.top Were all 1800 methanol molecules properly inserted here? Note that genbox does not update the topology automatically for any molecules other than water. > (d) grompp -f ions.mdp -c his8_meoh.gro -p topol.top -o ions.tpr -p topol.top > (e) genion -s ions.tpr -o added_ions.gro -p topol.top -pname NA -nname OH -nn 8 Per the genion help information, it is not well-suited to inserting polyatomic ions. Also, what are you choosing to replace here? genion is designed to replace water molecules with monoatomic ions, but you haven't added any water yet. If you're simply replacing elements of the "System" group, you've probably got fractional species somewhere. I would be willing to bet that this process is what is causing your problem. Check the contents of the coordinate file and topology before and after genion, and you will probably find the problem. Solution: don't use genion. Use genbox -ci -nmol to add your 8 OH molecules. -Justin > (f) genbox -cp added_ions.gro -cs tip4p.gro -o his8_meohi_wat.gro -p topol.top > Commands (a)-(f), all goes smooth. > > When I do the following > grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr > > I run into error which says moleculetype OH not found. > > > Added the following specifically in .top file > [ moleculetype ] > ; molname nrexcl > OH1 > > [atoms] > 1 OH 1 OH OH 1 0.21 1.008 ; > 2 OW 1 OH OW 1 -1.2115.4 ; > [ bonds ] > OW HW1gb_38 > > Going back to the command > grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr > > runs into different error as mentioned earlier : Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519) > > The .top file includes tip4p.itp, methanol.itp and ions.itp. > > So I am totally confused as to where I am going wrong. > Please guide. > > Thanks, > Shivangi > > > > Shivangi Nangia > Garrison Group > Graduate Student > 201A Chemistry Building > University Park PA 16802 > > > > > > > > > Hello, > > > > Thanks a lot for the suggestion. > > > > I think I made some progress but I am not there yet. > > > > I added the following in the ions.itp file > > > > [ moleculetype ] > > ; molname nrexcl > > OH1 > > > > [ atoms ] > > ; id at type res nr residu name at name cg nr charge > > 1 OH 1 OHOH 1 0 > > 1 OW 1 OWOW 1 -1 > > > > > > Still I ran into the same error that it could not find moleculetype OH. > > > > Than I specifically added the following to the .top file > > > > [ moleculetype ] > > ; molname nrexcl > > OH1 > > > > [atoms] > > 1 OH 1 OH OH 1 0.21 1.008 ; > > 2 OW 1 OH OW 1 -1.2115.4 ; > > [ bonds ] > >OW HW1gb_38 > > > > This helped. > > However, there is new error I am running into which says: > > Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519) > > > > I am trying to add 8 hydroxide ions in my methanol-water system. > > > > And how
Re: Re: Re: [gmx-users] Hydroixde Ion
Hi again, I have the following: I have not changed anything in ffG53a6.atp and .rtp As suggested by gmx users, I have the following in the ions,itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH 1 0 1 OW 1 OWOW 1 -1 I executed the following commands: (a) pdb2gmx -f his8.pdb -ignh -ter -his -p topol.top -o his8.gro (b) editconf -f his8.gro -box 5 5 5 -o his8box.gro (c) genbox -cp his8box.gro -ci 1methanol.gro -nmol 1800 -o his8_meoh.gro -p topol.top (d) grompp -f ions.mdp -c his8_meoh.gro -p topol.top -o ions.tpr -p topol.top (e) genion -s ions.tpr -o added_ions.gro -p topol.top -pname NA -nname OH -nn 8 (f) genbox -cp added_ions.gro -cs tip4p.gro -o his8_meohi_wat.gro -p topol.top Commands (a)-(f), all goes smooth. When I do the following grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr I run into error which says moleculetype OH not found. Added the following specifically in .top file [ moleculetype ] ; molname nrexcl OH1 [atoms] 1 OH 1 OH OH 1 0.21 1.008 ; 2 OW 1 OH OW 1 -1.21 15.4 ; [ bonds ] OW HW1gb_38 Going back to the command grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr runs into different error as mentioned earlier : Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519) The .top file includes tip4p.itp, methanol.itp and ions.itp. So I am totally confused as to where I am going wrong. Please guide. Thanks, Shivangi Shivangi Nangia Garrison Group Graduate Student 201A Chemistry Building University Park PA 16802 > Hello, > > Thanks a lot for the suggestion. > > I think I made some progress but I am not there yet. > > I added the following in the ions.itp file > > [ moleculetype ] > ; molname nrexcl > OH1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > 1 OH 1 OHOH 1 0 > 1 OW 1 OWOW 1 -1 > > > Still I ran into the same error that it could not find moleculetype OH. > > Than I specifically added the following to the .top file > > [ moleculetype ] > ; molname nrexcl > OH1 > > [atoms] > 1 OH 1 OH OH 1 0.21 1.008 ; > 2 OW 1 OH OW 1 -1.2115.4 ; > [ bonds ] >OW HW1gb_38 > > This helped. > However, there is new error I am running into which says: > Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519) > > I am trying to add 8 hydroxide ions in my methanol-water system. > And how are you attempting this? What command(s) did you give? What subsequent modifications to your topology did you make? The generic solution to your problem can be found here: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology > The confusion I have is: > The .gro file has OH but is gromacs really accounting OH as 2 atoms? Gromacs assigns parameters to the molecules it finds based on the entries in the respective [moleculetypes]. If you tell grompp or any other program that the [moleculetype] "OH" is comprised of two atoms, then there's no reason to believe anything is wrong. > Also, the difference (12519-12487) is greater than 8. > Without some context as to what you're doing and what you've done up to this point, this information does not lead to any useful solution. The number of molecules (either methanol or OH) in your topology does not match the contents of your coordinate file. -Justin > Kindly help. > > Thanks, > Shivangi > > > > Shivangi Nangia > Garrison Group > Graduate Student > 201A Chemistry Building > University Park PA 16802 > > On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote: > > Hello, > > > > I am new gromacs user. > > I am trying to set up a water-methanol system with few hyrdroxide ions. > > > > Since hyrdroxide ion does not already exist in gromacs database, I defined > the following in the .rtp file ( I am using ffG53a6) > > > > [ OH ] > > [ atoms ] > >OWOW-1.41000 0 > > HW1 H 0.41000 0 > > [ bonds ] > >OW HW1gb_38 > > [ angles ] > > ; aiajak gromos typpe > > [ impropers ] > > ; aiajakal gromos type > > [ dihedrals ] > > ; aiajakal gromos type > > That's only useful for pdb2gmx when generating .top files. > > > I also inclu
Re: Re: [gmx-users] Hydroixde Ion
Hello, Thanks a lot for the suggestion. I think I made some progress but I am not there yet. I added the following in the ions.itp file [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH 1 0 1 OW 1 OWOW 1 -1 Still I ran into the same error that it could not find moleculetype OH. Than I specifically added the following to the .top file [ moleculetype ] ; molname nrexcl OH1 [atoms] 1 OH 1 OH OH 1 0.21 1.008 ; 2 OW 1 OH OW 1 -1.2115.4 ; [ bonds ] OW HW1gb_38 This helped. However, there is new error I am running into which says: Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519) I am trying to add 8 hydroxide ions in my methanol-water system. The confusion I have is: The .gro file has OH but is gromacs really accounting OH as 2 atoms? Also, the difference (12519-12487) is greater than 8. Kindly help. Thanks, Shivangi Shivangi Nangia Garrison Group Graduate Student 201A Chemistry Building University Park PA 16802 On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote: > Hello, > > I am new gromacs user. > I am trying to set up a water-methanol system with few hyrdroxide ions. > > Since hyrdroxide ion does not already exist in gromacs database, I defined the following in the .rtp file ( I am using ffG53a6) > > [ OH ] > [ atoms ] >OWOW-1.41000 0 > HW1 H 0.41000 0 > [ bonds ] >OW HW1gb_38 > [ angles ] > ; aiajak gromos typpe > [ impropers ] > ; aiajakal gromos type > [ dihedrals ] > ; aiajakal gromos type That's only useful for pdb2gmx when generating .top files. > I also included OH in the .atp file ( I realise that hydroxide ion is NOT an atom, its a diatomic anion, I was just trying!) Don't. The .atp defines *atom* types. > I ran into the error: No such moleculetype OH > > I further included information in the ions.itp as follows: > > [ moleculetype ] > ; molname nrexcl > OH1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > 1 OH 1 OHOH 1 -1 Use two atoms, like you did for your .rtp entry. > The genion adds the "OH" in the .gro file and also the topol.top but when I try to minimize the system using > grompp -f minim.mdp -c 5his8_meohi_wat.gro -p topol.top -o em.tpr > I am still running into the same error, No such moleculetype OH. Your .top still does not have a functional [ moleculetype ] OH. You're probably not using the #include "ions.itp" mechanism correctly. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Hydroixde Ion
Hello, I am new gromacs user. I am trying to set up a water-methanol system with few hyrdroxide ions. Since hyrdroxide ion does not already exist in gromacs database, I defined the following in the .rtp file ( I am using ffG53a6) [ OH ] [ atoms ] OWOW-1.41000 0 HW1 H 0.41000 0 [ bonds ] OW HW1gb_38 [ angles ] ; aiajak gromos typpe [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type I also included OH in the .atp file ( I realise that hydroxide ion is NOT an atom, its a diatomic anion, I was just trying!) I ran into the error: No such moleculetype OH I further included information in the ions.itp as follows: [ moleculetype ] ; molname nrexcl OH1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OHOH 1 -1 The genion adds the "OH" in the .gro file and also the topol.top but when I try to minimize the system using grompp -f minim.mdp -c 5his8_meohi_wat.gro -p topol.top -o em.tpr I am still running into the same error, No such moleculetype OH. Any help will be greatly appreciated to help me understand. Thanks, Shivangi Shivangi Nangia Garrison Group Graduate Student 201A Chemistry Building University Park PA 16802 -- 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
