Re: [gmx-users] Re: Simulation of 2D lattice model
Justin, I want to simulate lattice with flexible nodes ( to examine fluctuations of that system by mens of Normal Mode Analysis). If I choose sp3 carbons as the nodes I obtain such lattice. But In that system hydrogens are also present which are not desirable in my system ( i want system consisted of only one type of atoms). On contrary if I choose sp2 hydrogens as the nodes I obtain completely rigid lattice which are not suitable for me. I suppose that united-atom model could be suitable for such flexible lattice but I've failed to apply g_x2top on my lattice with gromos force field ( I have no problems with the opls-aa for this system). Here I've obtain errors like Can not find forcefield for atom C116-70 with 3 bonds Can not find forcefield for atom C119-71 with 3 bonds Can not find forcefield for atom C120-72 with 3 bonds Can not find forcefield for atom C121-73 with 3 bonds Can not find forcefield for atom C122-74 with 3 bonds Can not find forcefield for atom C124-75 with 3 bonds Can not find forcefield for atom C125-76 with 3 bonds Can not find forcefield for atom C126-77 with 3 bonds Can not find forcefield for atom C127-78 with 3 bonds Can not find forcefield for atom H01-79 with 0 bonds Can not find forcefield for atom H02-80 with 0 bonds Can not find forcefield for atom H03-81 with 0 bonds Can not find forcefield for atom H04-82 with 0 bonds Can not find forcefield for atom H05-83 with 0 bonds So it seems that the bonds between C and H atoms were not recognized correclty in case of gromos-ff. Must the some corrections be done in the atomname2type.n2t file ? James 2013/1/2, Justin Lemkul : > > > On 1/2/13 3:08 PM, James Starlight wrote: >> Justin, >> >> I want to simulate flexible lattice consist of only one type of atoms >> (nodes). So the planar (sp2 ) carbons are rigid. On other hand more >> flexible (sp3) carbons connected with hydrogens but I want that >> hydrogens were not included in my lattice. Should I use another >> (what? )atom-type for the node of my lattice ? >> > > I'm sorry to say I don't understand what you're saying. If you want a > lattice > of carbon atoms, you can surely develop a united-atom model of such a > lattice > and never involve hydrogen atoms of any sort. Again, valence depends > entirely > upon what you define in the topology or its precursors (.n2t or .rtp). > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users 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
Fw: [gmx-users] Amidated C-terminal
The version of GROMACS I'm using is 4.5.5. I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for carbonyl C. Is there any problem with the C36 which I use? [ SER ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 0.05 4 HB1 HA 0.09 5 HB2 HA 0.09 6 OG OH1 -0.66 7 HG1 H 0.43 8 C C 0.51 9 O O -0.51 10 Sincerely, Shima From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Wednesday, January 2, 2013 10:46 PM Subject: Re: [gmx-users] Amidated C-terminal On 1/2/13 2:07 PM, Shima Arasteh wrote: > > > Hi, > > In order to make an amidated c-terminal, I used CT2 in charmm ff at the > c-terminal. The last residue of my peptide is serine, and the total charge of > peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the > c-terminal, and then getting top file, when I see the top file, everything is > ok up to the amidated serine residue. But something wrong is with the charged > amidated serine; the total charge is not equal to 5.00 : > > . > . > . > 361 C 22 LYS C 361 0.51 12.011 ; qtot >5.51 > 362 O 22 LYS O 362 -0.51 15.999 ; qtot >5 > ; residue 23 SER rtp SER q -0.0 > 363 NH1 23 SER N 363 -0.47 14.007 ; qtot >4.53 > 364 H 23 SER HN 364 0.31 1.008 ; qtot >4.84 > 365 CT1 23 SER CA 365 0.07 12.011 ; qtot >4.91 > 366 HB 23 SER HA 366 0.09 1.008 ; qtot >5 > 367 CT2 23 SER CB 367 0.05 12.011 ; qtot >5.05 > 368 HA 23 SER HB1 368 0.09 1.008 ; qtot >5.14 > 369 HA 23 SER HB2 369 0.09 1.008 ; qtot >5.23 > 370 OH1 23 SER OG 370 -0.66 15.999 ; qtot >4.57 > 371 H 23 SER HG1 371 0.43 1.008 ; qtot >5 > 372 C 23 SER C 372 0.51 12.011 ; qtot >5.51 > 373 NH2 23 SER NT 373 -0.62 14.007 ; qtot >4.89 > 374 H 23 SER HT1 374 0.3 1.008 ; qtot >5.19 > 375 H 23 SER HT2 375 0.32 1.008 ; qtot >5.51 > 376 O 23 SER O 376 -0.55 15.999 ; qtot >4.96 > > I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last > residue is positive charged? Do the defined atom charges are supposed to be > modified in last residue ? > The choice of CT2 is correct. The net charge comes from an incorrect charge assignment to the carbonyl C (atom 372), which should be +0.55 instead of +0.51, which is the charge in a normal backbone peptide bond. The aminoacids.c.tdb file correctly assigns this charge, so I don't know why pdb2gmx didn't produce it. I tried a protein in version 4.5.5 and it worked perfectly - which version are you using? If it's not 4.5.5, upgrade and try again. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Amidated C-terminal
The version of GROMACS I'm using is 4.5.5. I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for carbonyl C. Is there any problem with the C36 which I use? [ SER ] [ atoms ] N NH1 -0.47 0 HN H 0.31 1 CA CT1 0.07 2 HA HB 0.09 3 CB CT2 0.05 4 HB1 HA 0.09 5 HB2 HA 0.09 6 OG OH1 -0.66 7 HG1 H 0.43 8 C C 0.51 9 O O -0.51 10 Sincerely, Shima From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Wednesday, January 2, 2013 10:46 PM Subject: Re: [gmx-users] Amidated C-terminal On 1/2/13 2:07 PM, Shima Arasteh wrote: > > > Hi, > > In order to make an amidated c-terminal, I used CT2 in charmm ff at the > c-terminal. The last residue of my peptide is serine, and the total charge of > peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the > c-terminal, and then getting top file, when I see the top file, everything is > ok up to the amidated serine residue. But something wrong is with the charged > amidated serine; the total charge is not equal to 5.00 : > > . > . > . > 361 C 22 LYS C 361 0.51 12.011 ; qtot >5.51 > 362 O 22 LYS O 362 -0.51 15.999 ; qtot >5 > ; residue 23 SER rtp SER q -0.0 > 363 NH1 23 SER N 363 -0.47 14.007 ; qtot >4.53 > 364 H 23 SER HN 364 0.31 1.008 ; qtot >4.84 > 365 CT1 23 SER CA 365 0.07 12.011 ; qtot >4.91 > 366 HB 23 SER HA 366 0.09 1.008 ; qtot >5 > 367 CT2 23 SER CB 367 0.05 12.011 ; qtot >5.05 > 368 HA 23 SER HB1 368 0.09 1.008 ; qtot >5.14 > 369 HA 23 SER HB2 369 0.09 1.008 ; qtot >5.23 > 370 OH1 23 SER OG 370 -0.66 15.999 ; qtot >4.57 > 371 H 23 SER HG1 371 0.43 1.008 ; qtot >5 > 372 C 23 SER C 372 0.51 12.011 ; qtot >5.51 > 373 NH2 23 SER NT 373 -0.62 14.007 ; qtot >4.89 > 374 H 23 SER HT1 374 0.3 1.008 ; qtot >5.19 > 375 H 23 SER HT2 375 0.32 1.008 ; qtot >5.51 > 376 O 23 SER O 376 -0.55 15.999 ; qtot >4.96 > > I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last > residue is positive charged? Do the defined atom charges are supposed to be > modified in last residue ? > The choice of CT2 is correct. The net charge comes from an incorrect charge assignment to the carbonyl C (atom 372), which should be +0.55 instead of +0.51, which is the charge in a normal backbone peptide bond. The aminoacids.c.tdb file correctly assigns this charge, so I don't know why pdb2gmx didn't produce it. I tried a protein in version 4.5.5 and it worked perfectly - which version are you using? If it's not 4.5.5, upgrade and try again. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI segmentation Fault
Dear Justin, I will try your suggestion to rerun it on Berendsen coupling and see if there is any further problems. The system indeed contain the star shaped structure I showed you earlier (running multiple versions, containing from 1, 5, 10, 15 and 20 stars in a solvent box), the solvent is just martini defined water system. The first 50 beads of all 4 arms has hydrophobic interaction with the Water solvent. and the last 5 remaining beads on all 4 arms are set to have extreme similar hydrophilic interaction with martini water bead. Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:43 PM, Xu Dong Huang wrote: > @Justin, > > forgot to mention, yes the NVT was ran using MPI as well. (You're right, the > MPI is not the issue, because I took the file off my cluster and attempted to > run NPT on my personal computer, it reported same segmentation error, fault > 11) > > Xu Dong Huang > Chemical & Biochemical Engineering > Rutgers School of Engineering > xudo...@eden.rutgers.edu > > On Jan 2, 2013, at 3:34 PM, Justin Lemkul wrote: > >> >> >> On 1/2/13 3:20 PM, Xu Dong Huang wrote: >>> Dear gromac users, >>> >>> after examining my nvt run outcome, I see that my molecule has half of the >>> arm stuck outside of the box (I guess my run wasn't very successful). But I >>> thought the jumping outside of the box would be corrected by periodic >>> boundary? Should I run my nvt for longer since the structure itself did not >>> seem to change much in the solute? (My initial >>> Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? >>> if that resolves the problem at all that is) >>> >> >> There is no "outside" of a periodic cell, so this is a non-problem. Was the >> NVT run done in parallel? If it was, it eliminates a faulty MPI >> installation. If not, then that's an easily testable variable to determine >> the problem with NPT. You haven't posted any .mdp files, which is another >> variable in determining the viability of any simulation. >> >> -Justin >> >>> Thanks for any input, >>> >>> Chemical & Biochemical Engineering >>> Rutgers School of Engineering >>> xudo...@eden.rutgers.edu >>> >>> On Jan 2, 2013, at 3:08 PM, Xu Dong Huang wrote: >>> Dear gromac users, after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: Getting Loaded... Reading file npt.tpr, VERSION 4.5.3 (single precision) Loaded with Money WARNING: This run will generate roughly 3890 Mb of data starting mdrun 'star' 100 steps, 2.0 ps. step 0[Ultranode02:26884] *** Process received signal *** [Ultranode02:26884] Signal: Segmentation fault (11) [Ultranode02:26884] Signal code: Address not mapped (1) [Ultranode02:26884] Failing at address: 0x1f5acf020 [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] [Ultranode02:26884] *** End of error message *** /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault mdrun_mpi -v -deffnm npt -Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors) Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.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 >>> >> >> -- >> >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)sub
Re: [gmx-users] MPI segmentation Fault
On 1/2/13 3:42 PM, Xu Dong Huang wrote: @Justin, here are the details of my NVT and NPT .mdp, (All ran without position restraint) , + details of the NVT run For NVT.mdp: integrator = md tinit= 0.0 dt = 0.02 nsteps = 1 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 nstxtcout= 1000 xtc_precision= 100 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 For NPT.mdp integrator = md tinit= 0.0 dt = 0.02 nsteps = 100 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 nstxtcout= 1000 xtc_precision= 100 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p= 5.0 compressibility = 3e-4 ref_p= 1.0 Parrinello-Rahman is a really bad choice for the first phase of NPT equilibration for all but the most robust systems. It allows for rather wide box oscillations if the system is far from equilibrium. Try a weak coupling method (Berendsen) to see if it runs, then move to P-R if things are stable. What all is in the system? Is this that star-shaped structure you posted about previously? Any solvent? A full description would be really helpful. -Justin gen_vel = no gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 OUTPUT log FOR NVT RUN: Writing checkpoint, step 9760 at Wed Jan 2 06:43:55 2013 Step Time Lambda 1 200.00.0 Writing checkpoint, step 1 at Wed Jan 2 06:56:58 2013 Energies (kJ/mol) BondLJ (SR) Coulomb (SR) PotentialKinetic En. 1.27815e+03 -2.21982e+070.0e+00 -2.21969e+072.99756e+06 Total Energy Conserved En.Temperature Pressure (bar) -1.91994e+07 -2.18426e+072.99676e+027.09077e+02 <== ### ==> < A V E R A G E S > <== ### ==> Statistics over 10001 steps using 1001 frames Energies (kJ/mol) BondLJ (SR) Coulomb (SR) PotentialKinetic En. 1.33393e+03 -2.22049e+070.0e+00 -2.22036e+072.98604e+06 Total Energy Conserved En.Temperature Pressure (bar) -1.92176e+07 -2.18431e+072.98524e+027.06152e+02 Total Virial (kJ/mol) -9.41186e+057.05498e+016.65566e+02 7.05612e+01 -9.40675e+05 -3.05521e+00 6.65543e+02 -3.06027e+00 -9.44794e+05 Pressure (bar) 7.05835e+02 -4.93053e-02 -2.47918e-01 -4.93095e-027.05573e+02 -4.79105e-03 -2.47909e-01 -4.78920e-037.07047e+02 Total Dipole (D) 0.0e+000.0e+000.0e+00 Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:20 PM, Xu Dong Huang wrot
Re: [gmx-users] MPI segmentation Fault
@Justin, forgot to mention, yes the NVT was ran using MPI as well. (You're right, the MPI is not the issue, because I took the file off my cluster and attempted to run NPT on my personal computer, it reported same segmentation error, fault 11) Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:34 PM, Justin Lemkul wrote: > > > On 1/2/13 3:20 PM, Xu Dong Huang wrote: >> Dear gromac users, >> >> after examining my nvt run outcome, I see that my molecule has half of the >> arm stuck outside of the box (I guess my run wasn't very successful). But I >> thought the jumping outside of the box would be corrected by periodic >> boundary? Should I run my nvt for longer since the structure itself did not >> seem to change much in the solute? (My initial >> Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? >> if that resolves the problem at all that is) >> > > There is no "outside" of a periodic cell, so this is a non-problem. Was the > NVT run done in parallel? If it was, it eliminates a faulty MPI > installation. If not, then that's an easily testable variable to determine > the problem with NPT. You haven't posted any .mdp files, which is another > variable in determining the viability of any simulation. > > -Justin > >> Thanks for any input, >> >> Chemical & Biochemical Engineering >> Rutgers School of Engineering >> xudo...@eden.rutgers.edu >> >> On Jan 2, 2013, at 3:08 PM, Xu Dong Huang wrote: >> >>> Dear gromac users, >>> >>> after running a successful NVT, I was going to run NPT. (All ran with MPI), >>> however when I attempt to run the NPT, I get the following segmentation >>> error: >>> >>> Getting Loaded... >>> Reading file npt.tpr, VERSION 4.5.3 (single precision) >>> Loaded with Money >>> >>> >>> WARNING: This run will generate roughly 3890 Mb of data >>> >>> starting mdrun 'star' >>> 100 steps, 2.0 ps. >>> >>> step 0[Ultranode02:26884] *** Process received signal *** >>> [Ultranode02:26884] Signal: Segmentation fault (11) >>> [Ultranode02:26884] Signal code: Address not mapped (1) >>> [Ultranode02:26884] Failing at address: 0x1f5acf020 >>> [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] >>> [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] >>> [Ultranode02:26884] *** End of error message *** >>> /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 >>> Segmentation fault mdrun_mpi -v -deffnm npt >>> >>> >>> -Is my system blowing up? Or there is something wrong with MPI ? (I >>> requested 4 processors) >>> >>> Xu Dong Huang >>> Chemical & Biochemical Engineering >>> Rutgers School of Engineering >>> xudo...@eden.rutgers.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 >> > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI segmentation Fault
@Justin, here are the details of my NVT and NPT .mdp, (All ran without position restraint) , + details of the NVT run For NVT.mdp: integrator = md tinit= 0.0 dt = 0.02 nsteps = 1 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 nstxtcout= 1000 xtc_precision= 100 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 For NPT.mdp integrator = md tinit= 0.0 dt = 0.02 nsteps = 100 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 nstxtcout= 1000 xtc_precision= 100 xtc-grps = energygrps = system nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = V-rescale tc-grps = system tau_t= 1.0 ref_t= 300 Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p= 5.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 OUTPUT log FOR NVT RUN: Writing checkpoint, step 9760 at Wed Jan 2 06:43:55 2013 Step Time Lambda 1 200.00.0 Writing checkpoint, step 1 at Wed Jan 2 06:56:58 2013 Energies (kJ/mol) BondLJ (SR) Coulomb (SR) PotentialKinetic En. 1.27815e+03 -2.21982e+070.0e+00 -2.21969e+072.99756e+06 Total Energy Conserved En.Temperature Pressure (bar) -1.91994e+07 -2.18426e+072.99676e+027.09077e+02 <== ### ==> < A V E R A G E S > <== ### ==> Statistics over 10001 steps using 1001 frames Energies (kJ/mol) BondLJ (SR) Coulomb (SR) PotentialKinetic En. 1.33393e+03 -2.22049e+070.0e+00 -2.22036e+072.98604e+06 Total Energy Conserved En.Temperature Pressure (bar) -1.92176e+07 -2.18431e+072.98524e+027.06152e+02 Total Virial (kJ/mol) -9.41186e+057.05498e+016.65566e+02 7.05612e+01 -9.40675e+05 -3.05521e+00 6.65543e+02 -3.06027e+00 -9.44794e+05 Pressure (bar) 7.05835e+02 -4.93053e-02 -2.47918e-01 -4.93095e-027.05573e+02 -4.79105e-03 -2.47909e-01 -4.78920e-037.07047e+02 Total Dipole (D) 0.0e+000.0e+000.0e+00 Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:20 PM, Xu Dong Huang wrote: > Dear gromac users, > > after examining my nvt run outcome, I see that my molecule has half of the > arm stuck outside of the box (I guess my run wasn't very successful). But I > thought the jumping outside of the box would be corrected by periodic > boundary? Should I run my nvt for longer since the structure itself did not > seem to change much in the solute? (My initial > Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? if > that resolves the problem at all that is) >
Re: [gmx-users] MPI segmentation Fault
On 1/2/13 3:20 PM, Xu Dong Huang wrote: Dear gromac users, after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? if that resolves the problem at all that is) There is no "outside" of a periodic cell, so this is a non-problem. Was the NVT run done in parallel? If it was, it eliminates a faulty MPI installation. If not, then that's an easily testable variable to determine the problem with NPT. You haven't posted any .mdp files, which is another variable in determining the viability of any simulation. -Justin Thanks for any input, Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:08 PM, Xu Dong Huang wrote: Dear gromac users, after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: Getting Loaded... Reading file npt.tpr, VERSION 4.5.3 (single precision) Loaded with Money WARNING: This run will generate roughly 3890 Mb of data starting mdrun 'star' 100 steps, 2.0 ps. step 0[Ultranode02:26884] *** Process received signal *** [Ultranode02:26884] Signal: Segmentation fault (11) [Ultranode02:26884] Signal code: Address not mapped (1) [Ultranode02:26884] Failing at address: 0x1f5acf020 [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] [Ultranode02:26884] *** End of error message *** /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault mdrun_mpi -v -deffnm npt -Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors) Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulation of 2D lattice model
On 1/2/13 3:08 PM, James Starlight wrote: Justin, I want to simulate flexible lattice consist of only one type of atoms (nodes). So the planar (sp2 ) carbons are rigid. On other hand more flexible (sp3) carbons connected with hydrogens but I want that hydrogens were not included in my lattice. Should I use another (what? )atom-type for the node of my lattice ? I'm sorry to say I don't understand what you're saying. If you want a lattice of carbon atoms, you can surely develop a united-atom model of such a lattice and never involve hydrogen atoms of any sort. Again, valence depends entirely upon what you define in the topology or its precursors (.n2t or .rtp). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI segmentation Fault
Dear gromac users, after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial Xu Dong Huangnvt nstep=1, should I increase it to resolve the problem? if that resolves the problem at all that is) Thanks for any input, Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 2, 2013, at 3:08 PM, Xu Dong Huang wrote: > Dear gromac users, > > after running a successful NVT, I was going to run NPT. (All ran with MPI), > however when I attempt to run the NPT, I get the following segmentation > error: > > Getting Loaded... > Reading file npt.tpr, VERSION 4.5.3 (single precision) > Loaded with Money > > > WARNING: This run will generate roughly 3890 Mb of data > > starting mdrun 'star' > 100 steps, 2.0 ps. > > step 0[Ultranode02:26884] *** Process received signal *** > [Ultranode02:26884] Signal: Segmentation fault (11) > [Ultranode02:26884] Signal code: Address not mapped (1) > [Ultranode02:26884] Failing at address: 0x1f5acf020 > [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] > [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] > [Ultranode02:26884] *** End of error message *** > /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 > Segmentation fault mdrun_mpi -v -deffnm npt > > > -Is my system blowing up? Or there is something wrong with MPI ? (I > requested 4 processors) > > Xu Dong Huang > Chemical & Biochemical Engineering > Rutgers School of Engineering > xudo...@eden.rutgers.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 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] MPI segmentation Fault
Dear gromac users, after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: Getting Loaded... Reading file npt.tpr, VERSION 4.5.3 (single precision) Loaded with Money WARNING: This run will generate roughly 3890 Mb of data starting mdrun 'star' 100 steps, 2.0 ps. step 0[Ultranode02:26884] *** Process received signal *** [Ultranode02:26884] Signal: Segmentation fault (11) [Ultranode02:26884] Signal code: Address not mapped (1) [Ultranode02:26884] Failing at address: 0x1f5acf020 [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0] [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509] [Ultranode02:26884] *** End of error message *** /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault mdrun_mpi -v -deffnm npt -Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors) Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.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: Simulation of 2D lattice model
Justin, I want to simulate flexible lattice consist of only one type of atoms (nodes). So the planar (sp2 ) carbons are rigid. On other hand more flexible (sp3) carbons connected with hydrogens but I want that hydrogens were not included in my lattice. Should I use another (what? )atom-type for the node of my lattice ? James 2013/1/2, Justin Lemkul : >> > > The valence of an atom is whatever you assign it in the topology. Carbon > atoms > can be planar, as in aromatic rings of amino acids, without any issue. > > -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Amidated C-terminal
On 1/2/13 2:07 PM, Shima Arasteh wrote: Hi, In order to make an amidated c-terminal, I used CT2 in charmm ff at the c-terminal. The last residue of my peptide is serine, and the total charge of peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the c-terminal, and then getting top file, when I see the top file, everything is ok up to the amidated serine residue. But something wrong is with the charged amidated serine; the total charge is not equal to 5.00 : . . . 361 C 22LYS C361 0.51 12.011 ; qtot 5.51 362 O 22LYS O362 -0.51 15.999 ; qtot 5 ; residue 23 SER rtp SER q -0.0 363NH1 23SER N363 -0.47 14.007 ; qtot 4.53 364 H 23SER HN364 0.31 1.008 ; qtot 4.84 365CT1 23SER CA365 0.07 12.011 ; qtot 4.91 366 HB 23SER HA366 0.09 1.008 ; qtot 5 367CT2 23SER CB367 0.05 12.011 ; qtot 5.05 368 HA 23SERHB1368 0.09 1.008 ; qtot 5.14 369 HA 23SERHB2369 0.09 1.008 ; qtot 5.23 370OH1 23SER OG370 -0.66 15.999 ; qtot 4.57 371 H 23SERHG1371 0.43 1.008 ; qtot 5 372 C 23SER C372 0.51 12.011 ; qtot 5.51 373NH2 23SER NT373 -0.62 14.007 ; qtot 4.89 374 H 23SERHT13740.3 1.008 ; qtot 5.19 375 H 23SERHT2375 0.32 1.008 ; qtot 5.51 376 O 23SER O376 -0.55 15.999 ; qtot 4.96 I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last residue is positive charged? Do the defined atom charges are supposed to be modified in last residue ? The choice of CT2 is correct. The net charge comes from an incorrect charge assignment to the carbonyl C (atom 372), which should be +0.55 instead of +0.51, which is the charge in a normal backbone peptide bond. The aminoacids.c.tdb file correctly assigns this charge, so I don't know why pdb2gmx didn't produce it. I tried a protein in version 4.5.5 and it worked perfectly - which version are you using? If it's not 4.5.5, upgrade and try again. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Amidated C-terminal
Hi, In order to make an amidated c-terminal, I used CT2 in charmm ff at the c-terminal. The last residue of my peptide is serine, and the total charge of peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the c-terminal, and then getting top file, when I see the top file, everything is ok up to the amidated serine residue. But something wrong is with the charged amidated serine; the total charge is not equal to 5.00 : . . . 361 C 22 LYS C 361 0.51 12.011 ; qtot 5.51 362 O 22 LYS O 362 -0.51 15.999 ; qtot 5 ; residue 23 SER rtp SER q -0.0 363 NH1 23 SER N 363 -0.47 14.007 ; qtot 4.53 364 H 23 SER HN 364 0.31 1.008 ; qtot 4.84 365 CT1 23 SER CA 365 0.07 12.011 ; qtot 4.91 366 HB 23 SER HA 366 0.09 1.008 ; qtot 5 367 CT2 23 SER CB 367 0.05 12.011 ; qtot 5.05 368 HA 23 SER HB1 368 0.09 1.008 ; qtot 5.14 369 HA 23 SER HB2 369 0.09 1.008 ; qtot 5.23 370 OH1 23 SER OG 370 -0.66 15.999 ; qtot 4.57 371 H 23 SER HG1 371 0.43 1.008 ; qtot 5 372 C 23 SER C 372 0.51 12.011 ; qtot 5.51 373 NH2 23 SER NT 373 -0.62 14.007 ; qtot 4.89 374 H 23 SER HT1 374 0.3 1.008 ; qtot 5.19 375 H 23 SER HT2 375 0.32 1.008 ; qtot 5.51 376 O 23 SER O 376 -0.55 15.999 ; qtot 4.96 I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last residue is positive charged? Do the defined atom charges are supposed to be modified in last residue ? Would you please give me suggestions? Thanks in advance. Sincerely, Shima -- 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] Phosphorylation
Hi, all. Does anybody know wether I have to put a phosphorylated residue in the kinase's activation loop (last example is pdbid 2Y94) or not, when I'm working with protein-inhibitor complex without any type of protein-protein interactions? Or it is necessary only when I'm working with p-p complexes? The maximum time of dynamics is 10 ns. Any suggestions or links will be appreciated! Thank you for reply! -- Nemo me impune lacessit -- 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] Re: grompp error
Dear Justin, Thank you for your helpful suggestion. Mijiddorj From: Justin Lemkul [via GROMACS] To: Mijiddorj Sent: Wednesday, January 2, 2013 11:10 PM Subject: Re: grompp error On 1/2/13 10:01 AM, Mijiddorj wrote: > Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run > grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code > file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more > information and tips for troubleshooting, please check the GROMACSwebsite at > http://www.gromacs.org/Documentation/ErrorsHow can I solve this?Mijiddorj > You named your ions wrong. Please read the help information from genion -h: "The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead!" Note that, if you are referring to my "Tutorial 1" on lysozyme, the naming issue is explained and the genion command should be copied verbatim, as I do not use any +/- signs in the -pname or -nname options. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list [hidden email] 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 [hidden email]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.n6.nabble.com/grompp-error-tp5004198p5004199.html To unsubscribe from grompp error, click here. NAML -- View this message in context: http://gromacs.5086.n6.nabble.com/grompp-error-tp5004198p5004204.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Simulation of 2D lattice model
On 1/2/13 10:14 AM, Bogdan Costescu wrote: On Wed, Jan 2, 2013 at 2:58 PM, James Starlight wrote: By the way now I'd like to simulate the same 2D flexible ( in non planar hybridization) lattice but consist of non-hydrogens atoms only ( only atoms forming lattice scaffold ). Does it possible to change Carbon atom-valence (from 4 to 3) preventing tetragonal-like geometry ( >c- ) or should I use anothe atom type for such lattice ? I can't imagine how it can be both "non planar hybridization" and "preventing tetragonal-like geometry", but maybe I don't understand your intentions. Assuming you do want a change in geometry - from tetragonal to planar - then you need to use different parameters to describe the different geometry, it's not only about changing valence. If you use OPLS-AA, this means a change of atom type from something like C sp3 (f.e. opls_139) to sp2 (f.e. opls_147) - both these types chosen for having zero charge. One must use the right atom type (for LJ purposes) in conjunction with correct bonded parameters. You can create whatever monster atom you choose with any arbitrary valence, as long as you create the right bonded parameters that govern its geometry. Since MD simulations don't explicitly consider valence, you can do whatever you want, in theory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulation of 2D lattice model
On Wed, Jan 2, 2013 at 2:58 PM, James Starlight wrote: > By the way now I'd like to simulate the same 2D flexible ( in non > planar hybridization) lattice but consist of non-hydrogens atoms only > ( only atoms forming lattice scaffold ). Does it possible to change > Carbon atom-valence (from 4 to 3) preventing tetragonal-like geometry > ( >c- ) or should I use anothe atom type for such lattice ? I can't imagine how it can be both "non planar hybridization" and "preventing tetragonal-like geometry", but maybe I don't understand your intentions. Assuming you do want a change in geometry - from tetragonal to planar - then you need to use different parameters to describe the different geometry, it's not only about changing valence. If you use OPLS-AA, this means a change of atom type from something like C sp3 (f.e. opls_139) to sp2 (f.e. opls_147) - both these types chosen for having zero charge. Cheers, Bogdan -- 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: Simulation of 2D lattice model
On 1/2/13 9:26 AM, James Starlight wrote: by the way also I'd like to know what options for the pbc should I specify that my system looked like infinite lattice in the x-y dims ? Do you want the lattice to be infinite or do you just want it to look like it's infinite? If you want an infinite lattice, you need to build it such that bonds can be formed across periodic boundaries, in conjunction with the .mdp keyword periodic_molecules set to "yes." This is the approach many people take when simulating graphene sheets or CNT. See the list archive for extensive discussions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulation of 2D lattice model
On 1/2/13 8:58 AM, James Starlight wrote: Bogdan, Thank you for explanation. Indeed the problem was in the LINCS constrains which was not required for the lattice system. By the way now I'd like to simulate the same 2D flexible ( in non planar hybridization) lattice but consist of non-hydrogens atoms only ( only atoms forming lattice scaffold ). Does it possible to change Carbon atom-valence (from 4 to 3) preventing tetragonal-like geometry ( >c- ) or should I use anothe atom type for such lattice ? The valence of an atom is whatever you assign it in the topology. Carbon atoms can be planar, as in aromatic rings of amino acids, without any issue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp error
On 1/2/13 10:01 AM, Mijiddorj wrote: Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/ErrorsHow can I solve this?Mijiddorj You named your ions wrong. Please read the help information from genion -h: "The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead!" Note that, if you are referring to my "Tutorial 1" on lysozyme, the naming issue is explained and the genion command should be copied verbatim, as I do not use any +/- signs in the -pname or -nname options. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp error
Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/ErrorsHow can I solve this?Mijiddorj -- View this message in context: http://gromacs.5086.n6.nabble.com/grompp-error-tp5004198.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: genbox did not run?
Thank you, I got it. Mijiddorj -- View this message in context: http://gromacs.5086.n6.nabble.com/genbox-did-not-run-tp5004186p5004197.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Simulation of 2D lattice model
by the way also I'd like to know what options for the pbc should I specify that my system looked like infinite lattice in the x-y dims ? James 2013/1/2, James Starlight : > Bogdan, > > Thank you for explanation. Indeed the problem was in the LINCS > constrains which was not required for the lattice system. > > By the way now I'd like to simulate the same 2D flexible ( in non > planar hybridization) lattice but consist of non-hydrogens atoms only > ( only atoms forming lattice scaffold ). Does it possible to change > Carbon atom-valence (from 4 to 3) preventing tetragonal-like geometry > ( >c- ) or should I use anothe atom type for such lattice ? > > James > > 2013/1/2, Bogdan Costescu : >> On Wed, Jan 2, 2013 at 1:15 PM, James Starlight >> wrote: >>> so why my simulation of the sp3 lattice have been crashed with the >>> links warnings ( which always tells about wrong geometry in topology)? >> >> I might have missed something from the beginning of this discussion... >> Why do you use LINCS with a lattice ? What do you expect to obtain ? >> LINCS is normally used to keep bonds at their equilibrium length. If >> you do this in a lattice, the degrees of freedom will be strongly >> reduced, due to the coupled/restricted motions. How does this >> influence what you want to observe ? If you are not interested in the >> flexibility of the lattice itself, have you considered freezing it ? >> >> Cheers, >> Bogdan >> -- >> 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] Re: Simulation of 2D lattice model
Bogdan, Thank you for explanation. Indeed the problem was in the LINCS constrains which was not required for the lattice system. By the way now I'd like to simulate the same 2D flexible ( in non planar hybridization) lattice but consist of non-hydrogens atoms only ( only atoms forming lattice scaffold ). Does it possible to change Carbon atom-valence (from 4 to 3) preventing tetragonal-like geometry ( >c- ) or should I use anothe atom type for such lattice ? James 2013/1/2, Bogdan Costescu : > On Wed, Jan 2, 2013 at 1:15 PM, James Starlight > wrote: >> so why my simulation of the sp3 lattice have been crashed with the >> links warnings ( which always tells about wrong geometry in topology)? > > I might have missed something from the beginning of this discussion... > Why do you use LINCS with a lattice ? What do you expect to obtain ? > LINCS is normally used to keep bonds at their equilibrium length. If > you do this in a lattice, the degrees of freedom will be strongly > reduced, due to the coupled/restricted motions. How does this > influence what you want to observe ? If you are not interested in the > flexibility of the lattice itself, have you considered freezing it ? > > Cheers, > Bogdan > -- > 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] Re: Simulation of 2D lattice model
On Wed, Jan 2, 2013 at 1:15 PM, James Starlight wrote: > so why my simulation of the sp3 lattice have been crashed with the > links warnings ( which always tells about wrong geometry in topology)? I might have missed something from the beginning of this discussion... Why do you use LINCS with a lattice ? What do you expect to obtain ? LINCS is normally used to keep bonds at their equilibrium length. If you do this in a lattice, the degrees of freedom will be strongly reduced, due to the coupled/restricted motions. How does this influence what you want to observe ? If you are not interested in the flexibility of the lattice itself, have you considered freezing it ? Cheers, Bogdan -- 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: Simulation of 2D lattice model
On 1/2/13 7:15 AM, James Starlight wrote: Justin, so why my simulation of the sp3 lattice have been crashed with the links warnings ( which always tells about wrong geometry in topology)? Incorrect geometry is not the only cause of LINCS warnings. I haven't seen nearly enough information to know what the cause of the problem is. also I've tried to paraetrize completely planar (sp2) lattice but obtain errors like that Can not find forcefield for atom C27-22 with 2 bonds Can not find forcefield for atom C28-23 with 3 bonds Can not find forcefield for atom C4-24 with 3 bonds Can not find forcefield for atom C15-25 with 3 bonds Can not find forcefield for atom C1-26 with 3 bonds Can not find forcefield for atom C39-27 with 3 bonds Can not find forcefield for atom C41-28 with 3 bonds Can not find forcefield for atom C30-29 with 3 bonds Can not find forcefield for atom C2-30 with 2 bonds Can not find forcefield for atom C5-31 with 2 bonds Can not find forcefield for atom C8-32 with 3 bonds Can not find forcefield for atom H22-33 with 0 bonds So I've decided that the atom names is also relevant besides the geometry which was correct in that case. No, the names don't matter. The program is simply telling you that you have some atoms that don't fit within the criteria of existing .n2t entries. You may have to write your own in order for the program to complete successfully. The H22 atom is particularly instructive - it says zero bonds, which means that it is not within the distance cutoff to be actually bonded to anything. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dodecahedron box
On 1/2/13 7:03 AM, Turgay Cakmak wrote: Dear gromacs users, I am trying to solvate several peptides (at a desired positions) in a dodecahedron box. I have done following steps; 1) editconf -f peptides.gro -o peptides_nb.gro -c -d 1.0 -bt dodecahedron 2) genbox -cp peptides_nb.gro -cs -o peptides_solv.gro -p topol.top 3) After adding ions, I did energy minimization. 4) trjconv -f minim.trr -pbc mol -ur compact -o trajout.gro -s minim.tpr After that, I looked the system in VMD: Water molecules are around the peptides in the dodecahedron shape. But, box still seems like a rectangular shape. Is it correct or am I doing something wrong? Totally normal. Refer to the numerous posts in the list archive on this topic. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulation of 2D lattice model
Justin, so why my simulation of the sp3 lattice have been crashed with the links warnings ( which always tells about wrong geometry in topology)? also I've tried to paraetrize completely planar (sp2) lattice but obtain errors like that Can not find forcefield for atom C27-22 with 2 bonds Can not find forcefield for atom C28-23 with 3 bonds Can not find forcefield for atom C4-24 with 3 bonds Can not find forcefield for atom C15-25 with 3 bonds Can not find forcefield for atom C1-26 with 3 bonds Can not find forcefield for atom C39-27 with 3 bonds Can not find forcefield for atom C41-28 with 3 bonds Can not find forcefield for atom C30-29 with 3 bonds Can not find forcefield for atom C2-30 with 2 bonds Can not find forcefield for atom C5-31 with 2 bonds Can not find forcefield for atom C8-32 with 3 bonds Can not find forcefield for atom H22-33 with 0 bonds So I've decided that the atom names is also relevant besides the geometry which was correct in that case. James 2013/1/2, Justin Lemkul : > > > On 1/2/13 4:36 AM, James Starlight wrote: >> Justin, >> >> >> I've already tried use g_x2top for the model of the system built from >> regularly spaced C-atoms ( with included hydrogens to specify sp3 >> hybridization). >> >> By means of that command I've created topology for my lattice with big >> force constant ( for the simulation of the very rigid structure) >> >> g_x2top -f lattice_h.pdb -o lattice.top -ff oplsaa -kb 50 -kt 4000 >> -kp 500 -remdih >> >> >> the main problem which I've forced is the the absence of >> automate-generated impropers. As the result my lattice model at the >> beginning of the simulation (langevin's dynamics, nvt) have been >> perturbed and simulation finished with alot of lincs warnings. How I >> oculd fix it ? Should I use another atom names in the initial model ( >> e.g from polar hydrogens )? >> > > A bunch of sp3 carbons with attached hydrogens will not have any impropers, > > because the carbon centers are not planar. Atom names are irrelevant; > g_x2top > will do what you tell it based on bonded geometry. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users 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] genbox did not run?
On 1/2/13 4:20 AM, Mijiddorj wrote: I am a new user of Gromacs, I have problem with genbox. When I run genbox following error occurred:Program genbox, VERSION 4.5.5Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output error:/home/mijiddorj/Desktop/Tutorial02/1AKI1.topFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/ErrorsHow can I fix this problem?Mijiddorj The specified file does not exist in the working directory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulation of 2D lattice model
On 1/2/13 4:36 AM, James Starlight wrote: Justin, I've already tried use g_x2top for the model of the system built from regularly spaced C-atoms ( with included hydrogens to specify sp3 hybridization). By means of that command I've created topology for my lattice with big force constant ( for the simulation of the very rigid structure) g_x2top -f lattice_h.pdb -o lattice.top -ff oplsaa -kb 50 -kt 4000 -kp 500 -remdih the main problem which I've forced is the the absence of automate-generated impropers. As the result my lattice model at the beginning of the simulation (langevin's dynamics, nvt) have been perturbed and simulation finished with alot of lincs warnings. How I oculd fix it ? Should I use another atom names in the initial model ( e.g from polar hydrogens )? A bunch of sp3 carbons with attached hydrogens will not have any impropers, because the carbon centers are not planar. Atom names are irrelevant; g_x2top will do what you tell it based on bonded geometry. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Simulation of 2D lattice model
Justin, I've already tried use g_x2top for the model of the system built from regularly spaced C-atoms ( with included hydrogens to specify sp3 hybridization). By means of that command I've created topology for my lattice with big force constant ( for the simulation of the very rigid structure) g_x2top -f lattice_h.pdb -o lattice.top -ff oplsaa -kb 50 -kt 4000 -kp 500 -remdih the main problem which I've forced is the the absence of automate-generated impropers. As the result my lattice model at the beginning of the simulation (langevin's dynamics, nvt) have been perturbed and simulation finished with alot of lincs warnings. How I oculd fix it ? Should I use another atom names in the initial model ( e.g from polar hydrogens )? James 2013/1/1, Justin Lemkul : > > > On 1/1/13 2:01 PM, James Starlight wrote: >> Have someone else any ideas how the topology for a simple 2D lattice >> could be done ?:) >> >> I've tried to build it manually but for the system of 48 nodes >> definition of the angles and impropers have appeared very routinely :( >> > > For regularly spaced atoms, g_x2top should do it. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users 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 did not run?
I am a new user of Gromacs, I have problem with genbox. When I run genbox following error occurred:Program genbox, VERSION 4.5.5Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output error:/home/mijiddorj/Desktop/Tutorial02/1AKI1.topFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/ErrorsHow can I fix this problem?Mijiddorj -- View this message in context: http://gromacs.5086.n6.nabble.com/genbox-did-not-run-tp5004186.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Linear CG beads, grompp doesn't work
I think your original problem is that you define only one charge group for the entire molecule/polymer. You need to define each bead in a separate charge group and things will be fine :)) you do not have charges anyways. As far as I know angles have never made martini unstable but the conventional dihedral potential are not suited for martini or any flexible molecule. XAvier. On Jan 2, 2013, at 4:55, Justin Lemkul wrote: > > > On 1/1/13 10:51 PM, Xu Dong Huang wrote: >> @Justin, >> >> Does the philosophy described in your tutorial apply to CG martini bead >> models where 1 bead describes the entire CO2 atom? (If I were to do that, >> assuming) > > Presumably. As long as you satisfy the criteria mentioned in the tutorial > (moment of inertia and total mass), you should be able to get it to work. > I've never dealt with polymers and have very little personal experience with > CG models, so I don't know if there are other methodological issues that one > might encounter. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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
