Re: [gmx-users] V(R) around protein
And I don't think g_sas would do what i want. It calculates the volume of the protein itself. I am interested in the V of space at a distance R from the surface of the protein, excluding the volume of the protein. In other words, i need the surface accessible volume as a function of distance from the surface of the protein. Nihal On Mon, Sep 12, 2011 at 6:42 PM, E. Nihal Korkmaz wrote: > R is any distance from the surface of the protein. > > > On Mon, Sep 12, 2011 at 6:31 PM, Mark Abraham wrote: > >> On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote: >> >>> Dear all, >>> >>> Is there any function to get the Volume around a peptide/protein as a >>> function of R? >>> The problem is g_rdf -surf doesn't have a volume correction factor, so my >>> aim is to apply a volume correction factor manually by having V(R) around >>> the protein. >>> >> >> You haven't said what R is, but g_sas will calculate some volumes. >> >> Mark >> -- >> 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> >> > > > > -- > Elif Nihal Korkmaz > > Research Assistant > University of Wisconsin - Biophysics > Member of Qiang Cui & Thomas Record Labs > 1101 University Ave, Rm. 8359 > Madison, WI 53706 > Phone: 608-265-3644 > Email: kork...@wisc.edu > > > -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] V(R) around protein
R is any distance from the surface of the protein. On Mon, Sep 12, 2011 at 6:31 PM, Mark Abraham wrote: > On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote: > >> Dear all, >> >> Is there any function to get the Volume around a peptide/protein as a >> function of R? >> The problem is g_rdf -surf doesn't have a volume correction factor, so my >> aim is to apply a volume correction factor manually by having V(R) around >> the protein. >> > > You haven't said what R is, but g_sas will calculate some volumes. > > Mark > -- > 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> > -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] V(R) around protein
Dear all, Is there any function to get the Volume around a peptide/protein as a function of R? The problem is g_rdf -surf doesn't have a volume correction factor, so my aim is to apply a volume correction factor manually by having V(R) around the protein. Thanks, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] g_covar -xmpa
Dear all, Is there a "trick" to get the numbers for g_covar -xmpa? If not how can i calculate -xmpa results from -xpm -ascii results? Thanks Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] SPC/E water for Charmm ff implementation
Thanks but I already checked the literature. What I want to do is, to be able to trace down the parameters in the nonbonded file like it can be done for any version of gromos. There are slight changes among different force fields and I'd like to be able to find that. When I find where it reads spc/e parameters for c27, i want to play with the parameters that's why i am asking the file read. Thanks, Nihal On Wed, Jul 20, 2011 at 11:05 PM, Mark Abraham wrote: > On 21/07/2011 12:59 PM, E. Nihal Korkmaz wrote: > >> Dear all, >> >> I was trying to see the LJ parameters for SPC/E water in Charmm27.ff >> implementation in Gromacs. In the ffnonbonded.itp file i can see parameters >> for TIP3P, TIP4P, SPC but not for SPC/E. Does SPC/E use the same parameters >> with SPC? (but the charges listed in the ffnonbonded.itp is different than >> the ones listed in spce.itp) >> > > Why not check out the primary literature? Search GROMACS manual for SPC, > follow the reference link for the relevant citation. > > Mark > -- > 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> > -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] SPC/E water for Charmm ff implementation
Dear all, I was trying to see the LJ parameters for SPC/E water in Charmm27.ff implementation in Gromacs. In the ffnonbonded.itp file i can see parameters for TIP3P, TIP4P, SPC but not for SPC/E. Does SPC/E use the same parameters with SPC? (but the charges listed in the ffnonbonded.itp is different than the ones listed in spce.itp) Thanks, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] protein simulation w/ urea + water
Dear all, I am trying to simulate a protein in urea solution. I used *genbox -cp protein_in_box.gro -cs urea+h2o.gro -o out.gro -p topology* but the resulting topology doesn't contain any information on urea nor the atoms of urea. I also tried adding ureas on the protein with *-ci urea_single.gro -nmol some_number* option of genbox, that didn't give me the correct topology either. How should i create the correct topology? Thanks, Best regards, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] dodecahedron, octahedron box
Dear all, I am trying to solvate a protein in a dodecahedron box, and the box doesn't seem right. I tried *trjconv -s ur compact -pbc mol, *that ended up with a dodecahedron shaped water distrubution around the protein however the box is still shown as triclinic inbn Pymol? Is this Pymol's weakness or is this how dodecahedron works? Through the archive it sounds like genbox never ends up with an actual dodecahedron/octahedron box, Gromacs takes the triclinic box version to run simulation, is that right? If so how does the different box type take effect? I couldn't actually understand how does different box types are created/processed in Gromacs? Thanks, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] implicit solvent system set up
Dear all, This may sound stupid, but just to make sure that I am right track about implicit solvent simulations, the set up involves pdb2gmx editconf grompp I mean, we still need to define the box dimensions by editconf and apply periodicity, right? Besides, what type of ensemble would be a good choice (NPT, NVT, etc)? Best, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] Re: LINCS WARNING relative constraint deviation
What would you suggest as a short time step? I was using 0.002 ps. And just to make sure, would 5 ns of equilibration be enough for a ~110 amino acid long protein? Thanks, Nihal On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham wrote: > ** > On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote: > > I also checked the output of the minimization: > > Steepest Descents converged to machine precision in 402 steps, > but did not reach the requested Fmax < 10. > Potential Energy = -1.81875038188621e+04 > Maximum force = 3.20769543152855e+02 on atom 331 > Norm of force = 2.04356801849931e+01 > > I assume the structure is not relaxed enough to start a simulation. How can > I get it minimize further? I increased the step size up to 0.1 ps, i still > get the same result. > > > The minimization is probably OK, but a period of equilibration at a short > time step will probably help smooth the process out. Simulations in implicit > solvent have few explicit degrees of freedom compared to explicit solvent, > and might be rather more susceptible to equilibration issues if the > generated velocities are randomly not-quite-good-enough. > > Mark > > > Thanks, > Nihal > > On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz < > enihalkork...@gmail.com> wrote: > >> Dear all, >> >> I am trying to simulate a GB simulation of a 112 amino acid long protein. >> I keep getting these errors, >> >> Step 27718, time 55.436 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 33.319842, max 438.763717 (between atoms 79 and 81) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> >> Step 27718, time 55.436 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.058237, max 1.390675 (between atoms 91 and 93) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 91 92 50.20.1016 0.1065 0.1010 >> 91 93 90.00.1002 0.2415 0.1010 >> 91 94 70.20.1025 0.1066 0.1010 >> 79 80 90.00.1057 1.0667 0.1090 >> 79 81 90.01.3066 47.9342 0.1090 >> 85 86 90.00.1084 0.1758 0.1090 >> 85 87 90.01.0654 0.1668 0.1090 >> 88 89 90.00.1097 0.6994 0.1090 >> 88 90 90.00.1125 0.1097 0.1090 >> 91 92 50.20.1016 0.1065 0.1010 >> 91 93 90.00.1002 0.2415 0.1010 >> 91 94 70.20.1025 0.1066 0.1010 >> >> >> I am copying my mdp parameters below, I'd appreciate any suggestions to >> fix that. >> >> integrator = sd >> tinit= 0 >> dt = 0.002 >> nsteps = 250 >> simulation_part = 1 >> init_step= 1 >> >> nstxout = 5000 >> nstvout = 5000 >> nstenergy= 500 >> nstxtcout= 500 >> nstlog = 500 >> >> xtc_grps = System >> energygrps = System >> comm_mode= Linear >> ; neighbor searching and vdw/pme setting up >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> rlist= 2.0 >> >> implicit_solvent = GBSA >> gb_algorithm = OBC >> gb_saltconc = 0.15 >> rgbradii = 2.0 >> >> coulombtype = Cut-off >> fourierspacing = 0.1 >> pme_order= 6 >> rcoulomb = 2.0 >> >> vdwtype = Cut-off >> rvdw_switch = 1.0 >> rvdw = 2.0 >> >> ; cpt control >> tcoupl = V-rescale >> tc-grps = System >> tau_t= 0.1 >> ref_t= 300.0 >> >> Pcoupl = Berendsen >> pcoupltype = isotropic >> tau_p= 1.0 >> compressibility = 4.5e-5 >> ref_p= 1.0 >> >> ; velocity & temperature control >> gen_vel = yes >> gen_temp = 300.0 >> annealing= no >> constraints = hbonds >> constraint_algorithm = lincs >> morse= no >&
[gmx-users] Re: LINCS WARNING relative constraint deviation
I also checked the output of the minimization: Steepest Descents converged to machine precision in 402 steps, but did not reach the requested Fmax < 10. Potential Energy = -1.81875038188621e+04 Maximum force = 3.20769543152855e+02 on atom 331 Norm of force = 2.04356801849931e+01 I assume the structure is not relaxed enough to start a simulation. How can I get it minimize further? I increased the step size up to 0.1 ps, i still get the same result. Thanks, Nihal On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz wrote: > Dear all, > > I am trying to simulate a GB simulation of a 112 amino acid long protein. I > keep getting these errors, > > Step 27718, time 55.436 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 33.319842, max 438.763717 (between atoms 79 and 81) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > > Step 27718, time 55.436 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.058237, max 1.390675 (between atoms 91 and 93) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 91 92 50.20.1016 0.1065 0.1010 > 91 93 90.00.1002 0.2415 0.1010 > 91 94 70.20.1025 0.1066 0.1010 > 79 80 90.00.1057 1.0667 0.1090 > 79 81 90.01.3066 47.9342 0.1090 > 85 86 90.00.1084 0.1758 0.1090 > 85 87 90.01.0654 0.1668 0.1090 > 88 89 90.00.1097 0.6994 0.1090 > 88 90 90.00.1125 0.1097 0.1090 > 91 92 50.20.1016 0.1065 0.1010 > 91 93 90.00.1002 0.2415 0.1010 > 91 94 70.20.1025 0.1066 0.1010 > > > I am copying my mdp parameters below, I'd appreciate any suggestions to fix > that. > > integrator = sd > tinit= 0 > dt = 0.002 > nsteps = 250 > simulation_part = 1 > init_step= 1 > > nstxout = 5000 > nstvout = 5000 > nstenergy= 500 > nstxtcout= 500 > nstlog = 500 > > xtc_grps = System > energygrps = System > comm_mode= Linear > ; neighbor searching and vdw/pme setting up > nstlist = 10 > ns_type = grid > pbc = xyz > rlist= 2.0 > > implicit_solvent = GBSA > gb_algorithm = OBC > gb_saltconc = 0.15 > rgbradii = 2.0 > > coulombtype = Cut-off > fourierspacing = 0.1 > pme_order= 6 > rcoulomb = 2.0 > > vdwtype = Cut-off > rvdw_switch = 1.0 > rvdw = 2.0 > > ; cpt control > tcoupl = V-rescale > tc-grps = System > tau_t= 0.1 > ref_t= 300.0 > > Pcoupl = Berendsen > pcoupltype = isotropic > tau_p= 1.0 > compressibility = 4.5e-5 > ref_p= 1.0 > > ; velocity & temperature control > gen_vel = yes > gen_temp = 300.0 > annealing= no > constraints = hbonds > constraint_algorithm = lincs > morse= no > > > Thanks, > -- > Elif Nihal Korkmaz > > Research Assistant > University of Wisconsin - Biophysics > Member of Qiang Cui & Thomas Record Labs > 1101 University Ave, Rm. 8359 > Madison, WI 53706 > Phone: 608-265-3644 > Email: kork...@wisc.edu > > > -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] LINCS WARNING relative constraint deviation
Dear all, I am trying to simulate a GB simulation of a 112 amino acid long protein. I keep getting these errors, Step 27718, time 55.436 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 33.319842, max 438.763717 (between atoms 79 and 81) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 27718, time 55.436 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.058237, max 1.390675 (between atoms 91 and 93) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 91 92 50.20.1016 0.1065 0.1010 91 93 90.00.1002 0.2415 0.1010 91 94 70.20.1025 0.1066 0.1010 79 80 90.00.1057 1.0667 0.1090 79 81 90.01.3066 47.9342 0.1090 85 86 90.00.1084 0.1758 0.1090 85 87 90.01.0654 0.1668 0.1090 88 89 90.00.1097 0.6994 0.1090 88 90 90.00.1125 0.1097 0.1090 91 92 50.20.1016 0.1065 0.1010 91 93 90.00.1002 0.2415 0.1010 91 94 70.20.1025 0.1066 0.1010 I am copying my mdp parameters below, I'd appreciate any suggestions to fix that. integrator = sd tinit= 0 dt = 0.002 nsteps = 250 simulation_part = 1 init_step= 1 nstxout = 5000 nstvout = 5000 nstenergy= 500 nstxtcout= 500 nstlog = 500 xtc_grps = System energygrps = System comm_mode= Linear ; neighbor searching and vdw/pme setting up nstlist = 10 ns_type = grid pbc = xyz rlist= 2.0 implicit_solvent = GBSA gb_algorithm = OBC gb_saltconc = 0.15 rgbradii = 2.0 coulombtype = Cut-off fourierspacing = 0.1 pme_order= 6 rcoulomb = 2.0 vdwtype = Cut-off rvdw_switch = 1.0 rvdw = 2.0 ; cpt control tcoupl = V-rescale tc-grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; velocity & temperature control gen_vel = yes gen_temp = 300.0 annealing= no constraints = hbonds constraint_algorithm = lincs morse= no Thanks, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] load imbalance
Thanks for the reply. Would that cause any problems in the simulation? It says force 154.9%, does that mean it is applying the wrong force? Is it safe to proceed to simulation like that? Thanks, Nihal On Thu, Jun 16, 2011 at 9:54 PM, Mark Abraham wrote: > ** > On 17/06/2011 12:44 PM, E. Nihal Korkmaz wrote: > > Hi all, > > I am trying to run GB model simulation of a small protein. I keep getting > these errors for every step printed to the log file. > > DD load balancing is limited by minimum cell size in dimension X > DD step 35999 vol min/aver 0.799! load imb.: force 154.9% > > > Not all systems can efficiently parallelize on arbitrary numbers of > processors for a given implementation. There's an analysis at the top of the > .log file that describes the issues leading to the minimum cell size. > Possibly there's an issue there, but more likely you've got not enough work > for your processors. > > Mark > > > Below i copied my mdp parameters. I'd appreciate any suggestion to help me > fix this. > > Thanks, > Nihal > > > integrator = sd > tinit= 0 > dt = 0.002 > nsteps = 500 > simulation_part = 1 > init_step= 1 %start from 5ns > > > nstxout = 5000 > nstvout = 5000 > nstenergy= 500 > nstxtcout= 500 > nstlog = 500 > > xtc_grps = System > energygrps = System > comm_mode= Linear > ; neighbor searching and vdw/pme setting up > nstlist = 10 > ns_type = grid > pbc = xyz > rlist= 2.0 > > coulombtype = pme > fourierspacing = 0.1 > pme_order= 6 > rcoulomb = 2.0 > > vdwtype = Cut-off > rvdw_switch = 1.0 > rvdw = 2.0 > > ; cpt control > tcoupl = Berendsen > tc-grps = System > tau_t= 0.1 > ref_t= 300.0 > Pcoupl = Berendsen > pcoupltype = isotropic > tau_p= 1.0 > compressibility = 4.5e-5 > ref_p= 1.0 > > ; velocity & temperature control > gen_vel = yes > gen_temp = 300.0 > annealing= no > constraints = hbonds > constraint_algorithm = lincs > morse= no > > > -- > Elif Nihal Korkmaz > > Research Assistant > University of Wisconsin - Biophysics > Member of Qiang Cui & Thomas Record Labs > 1101 University Ave, Rm. 8359 > Madison, WI 53706 > Phone: 608-265-3644 > Email: kork...@wisc.edu > > > > > -- > 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 > -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] cross correlations
Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but that's not what i'm looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] load imbalance
Hi all, I am trying to run GB model simulation of a small protein. I keep getting these errors for every step printed to the log file. DD load balancing is limited by minimum cell size in dimension X DD step 35999 vol min/aver 0.799! load imb.: force 154.9% Below i copied my mdp parameters. I'd appreciate any suggestion to help me fix this. Thanks, Nihal integrator = sd tinit= 0 dt = 0.002 nsteps = 500 simulation_part = 1 init_step= 1 %start from 5ns nstxout = 5000 nstvout = 5000 nstenergy= 500 nstxtcout= 500 nstlog = 500 xtc_grps = System energygrps = System comm_mode= Linear ; neighbor searching and vdw/pme setting up nstlist = 10 ns_type = grid pbc = xyz rlist= 2.0 coulombtype = pme fourierspacing = 0.1 pme_order= 6 rcoulomb = 2.0 vdwtype = Cut-off rvdw_switch = 1.0 rvdw = 2.0 ; cpt control tcoupl = Berendsen tc-grps = System tau_t= 0.1 ref_t= 300.0 Pcoupl = Berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; velocity & temperature control gen_vel = yes gen_temp = 300.0 annealing= no constraints = hbonds constraint_algorithm = lincs morse= no -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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
