[gmx-users] gromacs
i used the pdb2gmx command but i get a message command not found. can you help me -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs
Set the installed path and library path of Gromacs in .bashrc file and source it On Tue, Apr 1, 2014 at 1:36 PM, Meenakshi Rajput ashi.rajpu...@gmail.comwrote: i used the pdb2gmx command but i get a message command not found. can you help me -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to provide the FFTW3 install directory
I don't know, I just follow the instruction. What information should I need to give? On Tue, Apr 1, 2014 at 1:55 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 01.04.2014 08:29, Ly Minh Nhat wrote: Well, I have solve the first error by installing g++. The fftw error still occurs: ... CMake Error at /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108 (message): Could not find FFTW3F. Provide the fftw3 install directory in the FFTW3F_ROOT_DIR environment variable. (missing: FFTW3F_LIBRARIES) Call Stack (most recent call first): /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315 (_FPHSA_FAILURE_MESSAGE) cmake/FindFFTW3F.cmake:31 (find_package_handle_standard_args) CMakeLists.txt:729 (find_package) Could not find FFTW3F Note the trailing F? Did you build the fftw3 or the fftw3f library (trailing f for 'float')? M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to provide the FFTW3 install directory
On 01.04.2014 10:36, Ly Minh Nhat wrote: I don't know, I just follow the instruction. What information should I need to give? It's on the fftw3 install page (http://www.fftw.org/doc/Installation-on-Unix.html) in the first item: • --enable-float: Produces a single-precision version of FFTW (float) instead of the default double-precision (double). M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs
Please please read the basics (i.e. how to use) about Gromacs before posting questions. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] exclude some frames from trajectory
dear users i am trying to make a .xtc file from an existing .trr and exclude some frams of .trr file. should i be using trajconv to cut the trajectory around the nonwanted frames and fuse the wanteds by trajcat? is there any other way to do it in a single command? regards, saman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] protein water contacts
Thank you Justin for your reply. Yes I am getting unfolded configurations at higher temperature (loss of native contacts and increase in Rg). I have used NPT ensemble. Is it that we cannot compare number of contacts at two different temperatures using NPT ensemble? Or is there any normalization factor that can account for the change in density? -- View this message in context: http://gromacs.5086.x6.nabble.com/protein-water-contacts-tp5015503p5015538.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Checking the possibility of one complex out of possible two
On 3/31/14, 10:29 PM, Pappu Kumar wrote: Decoupling seems only feasible for small ligands. I tried to decople a protein but the grompp does not converge. Could you tell me the maximum size of the molecule that is feasible for decoupling? I already calculated the free energy of solvation by APBS. Decoupling only works efficiently for small molecules. I don't know of a hard rule that defines what small is, but the more flexible the molecule is, the more difficult it becomes to deal with. Theoretically, you can make anything work, but convergence can be hard to attain for anything that is too large. -Justin Now I am pulling out one monomer from the other in both cases and checking the PMF along the trajectory using your tutorial on umbrella sampling. Thanks. On Monday, 31 March 2014 8:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/31/14, 6:07 AM, Pappu Kumar wrote: In the two protein dimers, the location of one monomer is at the opposite side of the other monomer : (| 0 and 0 |) when they are aligned (0 - common monomer, (| or |) the other monomer). So it would be hard to get the reaction coordinate for PMF calculation. I am wondering if I can compare the free energy of decoupling from water of two dimers separately by TI (g_bar). Can I use the same techinique in case of a point mutation? Thank you. Doubtful. Decoupling a whole protein is impractical from both a performance and analysis standpoint. The simulations will probably never reach convergence and will sample a bunch of really unphysical states. Something like MM/PBSA would be much more sensible. -Justin On Friday, 28 March 2014 7:40 AM, Justin Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 3/27/14, 1:59 PM, Pappu Kumar wrote: I got two long protein complexes made out of 20 monomers of ~300 residues. But only one complex exists biologically. I am trying to find out the energetically favourable complex by MD simulation in gromacs 4.6.5. Initially I took out a dimer from the complexes and ran steepest descent followed by L-BFGS minimization . Although the total energy was lower in one dimer, after the L-BFGS, the energy was similar. Then I ran 50ns MD simulation and calculated the interaction energies between the monomers which is similar in both cases. The idea was that in the wrong confomation the interaction energy would be lower. Now I am wondering how to find out the correct conformation between the two possibilites. I also checked the free energy of solvation which is different in both cases. I am not sure if it is a clear indicator of stability since entropy is not taken into account. Let me know if you have any ideas. I am planning to run coarse grained simulations in MARTINI. Thank you. Calculating an actual deltaG of binding (i.e. a PMF) between the two monomers is about the only legitimate way I can think of to do this. The values of potential energy in a minimized structure are totally dependent on the force field, as are the nonbonded interaction energies, which (more importantly) aren't necessarily parametrized to be anything useful. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu mailto:jalem...@outerbanks.umaryland.edu mailto:jalem...@outerbanks.umaryland.edu mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
Re: [gmx-users] Water out of box? Negative Z-Coordinates
Many thanks to both of you! :)
I am not that familiar with C-Code and gromacs. Maybe you could take a look
at it, that this would be correct for me? Does this code also work for none
cubic boxes?
// Here begins the actual analysis
static int analyze_frame(t_topology *top, t_trxframe *fr, t_pbc *pbc,
int nr, gmx_ana_selection_t *sel[], void *data)
{
const rvec *pos = fr-x;// positions
const int numAtoms = fr-natoms;// number of all atoms
const rvec box = { fr-box[XX][XX], fr-box[YY][YY], fr-box[ZZ][ZZ] };
// box size
// Do I have to change something in the next four lines according to my
code above?
matrix transp,invbox;
rvec tmp;
transpose(frame.box,transp);
m_inv(transp,invbox);
for (int i=0; inumAtoms; i++)
{
mvmul(invbox,fr.x[i],tmp); // Same question for the next five lines
tmp[0] -= floor(tmp[0]);
tmp[1] -= floor(tmp[1]);
tmp[2] -= floor(tmp[2]);
mvmul(transp,tmp,fr.x[i]);
}
}
After this code, do I have to work with the tmp or can I use my position
vector pos? E.g. z-coordinate of particle i is just
pos[i][ZZ];
Or the box size is
box[ZZ];
That is easy to understand for me and I would like to keep it that simple.
So if it changes the name e.g. from pos to pos2 would be nice :)
Many thanks to you Tsjerk Wassenaar!
--
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Re: [gmx-users] exclude some frames from trajectory
I would try this one: trjconv -f traj.trr -o traconv.xtc -b 0 -e 25 This line exports just the first frames from your trajectory traj.trr. Now you have the change the values behind -b and -e, depending on your settings. -- View this message in context: http://gromacs.5086.x6.nabble.com/exclude-some-frames-from-trajectory-tp5015536p5015543.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] difference in energy when using -nb cpu
Not so far. You are comparing the results of two different chaotic processes - see http://www.gromacs.org/Documentation/Terminology/Reproducibility Mark On Tue, Apr 1, 2014 at 1:05 AM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: Hi all, I am running a nvt position restrained equilibration step on a protein, with the native GPU accelerated run, I get Potential Energy = -5.4152162e+05 Maximum force = 2.4561725e+02 on atom 2350 Norm of force = 5.0402722e+00 but same .tpr file I get with -nb cpu Potential Energy = -5.4509656e+05 Maximum force = 1.5848671e+02 on atom 2350 Norm of force = 3.1396613e+00 Does this indicate I have bad combination of parameters? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Erro in SMD simulation..
Thank you Justin for your valuable reply. But you know, my box size is 17.744*17.744*17.744 nm^3. I have used editconf -bt cubic -f 20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6 to generate the box. And the full description of the box size I have used is Read 15484 atoms No velocities found system size : 7.604 8.101 13.546 (nm) diameter : 14.544 (nm) center : 2.405 3.212 -2.870 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 6.467 5.661 11.742 (nm) new center : 8.872 8.872 8.872 (nm) new box vectors : 17.744 17.744 17.744 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :5587.13 (nm^3) Please suggest me the better option for my system. Should I increase the d value? Actually, the whole system contains approximately 193000 atoms and whenever I am increasing the d value the atoms no. is increasing significantly. Is there any option which can allow me to increase the box size without increasing the number of solvent molecules? And one more more thing, is the cubic option fine? Thanks, Kalyan. On Tue, Apr 1, 2014 at 7:06 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5015544...@n6.nabble.com wrote: On 4/1/14, 6:16 AM, Kalyanashis wrote: Dear all, I am trying to run an SMD simulation of an enzyme system with a drug molecule. The final SMD run was crashed at the middle of the MD run(crashed at 1370 ps). I got an error and the erro is Fatal error: Distance of pull group 1 (8.662854 nm) is larger than 0.49 times the box size (8.832091) I have checked for the solution in the gromacs user forum( http://gromacs.5086.x6.nabble.com/Distance-of-pull-group-1-2-142226-nm-is-larger-than-0-49-times-the-box-size-2-184750-td5007938.html#a5007939, http://gromacs.5086.x6.nabble.com/Pull-code-with-pull-geometry-cylinder-generates-error-Distance-of-pull-group-1-4-030185-nm-is-larger-td5001603.html#a5001695) but I did get any information. I have attache my smd.mdp file title = 2JEY-HI6 cpp= /usr/bin/cpp constraints= all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 500 ; total 2 ns. nstcomm= 100 nstxout= 500; collect data every 1 ps ;nstxtcout = 500 ;xtc_precision = 1000 nstvout= 1000 nstfout= 0 nstenergy = 100 nstlog = 100 nstlist= 100 ns_type= grid pbc = xyz rlist = 1.0 coulombtype= PME rcoulomb = 1.0 vdwtype= cutoff rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.5 tcgrps = system ref_t = 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic ; Use semiisotropic when working with membranes tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord-scaling= all ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;COM pulling pull = umbrella pull_geometry= distance pull_dim = N N Y pull_r1 = 1 pull_r0 = 1 ;pull_constr_tot = 1e-6 pull_start = yes pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 ;name of reference group pull_group0 = Protein ;pull_weights = 0 ;name of pull group pull_group1 = UNK ;pull_weights = 0 pull_vec1= 0.0 0.0 -1 ;ref. distance at t=0 ;pull_init1 = -2.4477384 -1.0229216 -1.5900776 ;rate of change of ref. gr. [nm/ps] pull_rate1 = 0.0005 ;force constant [KJ mol^-1 nm^-2] pull_k1 = 1586.747 ;pull_kB1= I changed the pull_k1, added pbc=xyz but nothing is working. One of friend got same problem but pbc=xyz was working for his system. Please suggest me any probable solution. Your box is too small to pull as far as you have. With the distance geometry, the vector between the pulled and reference groups must always be less than half the shortest box vector among those used for pulling (in your case, just z). -Justin --
Re: [gmx-users] Erro in SMD simulation..
On 4/1/14, 12:56 PM, Kalyanashis wrote: Thank you Justin for your valuable reply. But you know, my box size is 17.744*17.744*17.744 nm^3. I have used editconf -bt cubic -f 20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6 to generate the box. And the full description of the box size I have used is Read 15484 atoms No velocities found system size : 7.604 8.101 13.546 (nm) diameter : 14.544 (nm) center : 2.405 3.212 -2.870 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 6.467 5.661 11.742 (nm) new center : 8.872 8.872 8.872 (nm) new box vectors : 17.744 17.744 17.744 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :5587.13 (nm^3) Please suggest me the better option for my system. Should I increase the d value? Actually, the whole system contains approximately 193000 atoms and whenever I am increasing the d value the atoms no. is increasing significantly. Is there any option which can allow me to increase the box size without increasing the number of solvent molecules? And one more more thing, is the cubic option fine? You're using pressure coupling so the box vectors change over time. The error complains because 8.662854 * 2 = 17.325708, which is totally feasible to expect for normal box vector fluctuations. A cubic box is usually the most inefficient shape for most systems. Depending on the symmetry of your system, you can probably do a lot better. If you're pulling only along z, then a rectangular box with a suitable z-dimension is probably the next easiest way to go and will save you a ton of unnecessary water molecules. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Erro in SMD simulation..
On 4/1/14, 2:18 PM, Kalyanashis wrote: Thank you so much Justin. Now I am trying with a rectangular box. I don not whether it will work or not. There shouldn't be any guesswork involved. You know what the initial COM separation is (or you can easily calculate it or wait for grompp to print it out), and you know from pull_rate1 and the number of steps what the maximum displacement should be, so you can plan accordingly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Erro in SMD simulation..
Thank you so much Justin. Now I am trying with a rectangular box. I don not whether it will work or not. On Tue, Apr 1, 2014 at 10:51 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5015553...@n6.nabble.com wrote: On 4/1/14, 12:56 PM, Kalyanashis wrote: Thank you Justin for your valuable reply. But you know, my box size is 17.744*17.744*17.744 nm^3. I have used editconf -bt cubic -f 20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6 to generate the box. And the full description of the box size I have used is Read 15484 atoms No velocities found system size : 7.604 8.101 13.546 (nm) diameter : 14.544 (nm) center : 2.405 3.212 -2.870 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 6.467 5.661 11.742 (nm) new center : 8.872 8.872 8.872 (nm) new box vectors : 17.744 17.744 17.744 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :5587.13 (nm^3) Please suggest me the better option for my system. Should I increase the d value? Actually, the whole system contains approximately 193000 atoms and whenever I am increasing the d value the atoms no. is increasing significantly. Is there any option which can allow me to increase the box size without increasing the number of solvent molecules? And one more more thing, is the cubic option fine? You're using pressure coupling so the box vectors change over time. The error complains because 8.662854 * 2 = 17.325708, which is totally feasible to expect for normal box vector fluctuations. A cubic box is usually the most inefficient shape for most systems. Depending on the symmetry of your system, you can probably do a lot better. If you're pulling only along z, then a rectangular box with a suitable z-dimension is probably the next easiest way to go and will save you a ton of unnecessary water molecules. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [hidden email] http://user/SendEmail.jtp?type=nodenode=5015553i=0 | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [hidden email]http://user/SendEmail.jtp?type=nodenode=5015553i=1. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Erro-in-SMD-simulation-tp5015535p5015553.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from Erro in SMD simulation.., click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5015535code=a2FseWFuLmNoZW0uaW5AZ21haWwuY29tfDUwMTU1MzV8NTkxMDYyNTYz . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- View this message in context: http://gromacs.5086.x6.nabble.com/Erro-in-SMD-simulation-tp5015535p5015556.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to provide the FFTW3 install directory
a) Did you mean build as make a build folder? If so, then yes. My process is mkdir build, cd bulid, cmake .., make, make install. b) I load enviroment variable during cmake: cmake .. -DCMAKE_PREFIX_PATH=/usr/local There is no output for source /usr/local/gromacs/bin/GMXRC ooker@ooker-Aspire-4741:~$ source /usr/local/gromacs/bin/GMXRC ooker@ooker-Aspire-4741:~$ There is GMXRC file in /usr/local/gromacs/bin. On Tue, Apr 1, 2014 at 10:36 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 01.04.2014 17:12, Ly Minh Nhat wrote: When I type which mdrun in the terminal, it does nothing ooker@ooker-Aspire-4741:~$ which mdrun ooker@ooker-Aspire-4741:~$ Did you (a) install gromacs after build? (b) load environment variables after install $ source /usr/local/gromacs/bin/GMXRC see: Getting access to GROMACS after installation in http://www.gromacs.org/Documentation/Installation_ Instructions_4.5#Final_Installation M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to provide the FFTW3 install directory
More info: after cmake successfully, during make I meet many warnings, one of them like this: /home/ooker/Desktop/gromacs-4.5.7/src/mdlib/forcerec.c: In function 'init_forcerec': /home/ooker/Desktop/gromacs-4.5.7/src/mdlib/forcerec.c:288:15: warning: 'tmp_charge[3]' may be used uninitialized in this function [-Wmaybe-uninitialized] if(tmp_charge[j] != solvent_parameters[k].charge[j]) ^ /home/ooker/Desktop/gromacs-4.5.7/src/mdlib/forcerec.c:171:23: note: 'tmp_charge[3]' was declared here real tmp_charge[4]; But it still continues. On Wed, Apr 2, 2014 at 2:10 AM, Ly Minh Nhat ganuongp...@gmail.com wrote: a) Did you mean build as make a build folder? If so, then yes. My process is mkdir build, cd bulid, cmake .., make, make install. b) I load enviroment variable during cmake: cmake .. -DCMAKE_PREFIX_PATH=/usr/local There is no output for source /usr/local/gromacs/bin/GMXRC ooker@ooker-Aspire-4741:~$ source /usr/local/gromacs/bin/GMXRC ooker@ooker-Aspire-4741:~$ There is GMXRC file in /usr/local/gromacs/bin. On Tue, Apr 1, 2014 at 10:36 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 01.04.2014 17:12, Ly Minh Nhat wrote: When I type which mdrun in the terminal, it does nothing ooker@ooker-Aspire-4741:~$ which mdrun ooker@ooker-Aspire-4741:~$ Did you (a) install gromacs after build? (b) load environment variables after install $ source /usr/local/gromacs/bin/GMXRC see: Getting access to GROMACS after installation in http://www.gromacs.org/Documentation/Installation_ Instructions_4.5#Final_Installation M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Projecting conformational changes onto PCs
Dear all, Is there any gromacs tool to project a given conformational change (i.e. the structural difference after superposing a given protein in conformation 1 onto conformation 2), on a set of already computed Principal components computed by g_covar? Or should I implement myself ? I would like to know which are the PCs that contribute the most to the the observed conformational change. Thanks so much in advance, Raul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to provide the FFTW3 install directory
On 01.04.2014 21:10, Ly Minh Nhat wrote: There is no output for source /usr/local/gromacs/bin/GMXRC ooker@ooker-Aspire-4741:~$ source /usr/local/gromacs/bin/GMXRC ooker@ooker-Aspire-4741:~$ There is GMXRC file in /usr/local/gromacs/bin. Yes. And after this 'source command', what does $ which mdrun say? M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Projecting conformational changes onto PCs
g_anaeig Cheers, Tsjerk On Tue, Apr 1, 2014 at 9:36 PM, Mendez Giraldez, Raul rmen...@email.unc.edu wrote: Dear all, Is there any gromacs tool to project a given conformational change (i.e. the structural difference after superposing a given protein in conformation 1 onto conformation 2), on a set of already computed Principal components computed by g_covar? Or should I implement myself ? I would like to know which are the PCs that contribute the most to the the observed conformational change. Thanks so much in advance, Raul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Projecting conformational changes onto PCs
Hi Tsjerk, Thanks for your answer, but g_anaeig (among other things) gives the projection of each snaphot of my trajectory onto the selected PCs along time. What I want is the projection of a different structure, for instance the difference between my protein into a closed conformation (different from the open conformation that I used in the MD simulations). Ideally I would have a Delta_R vector (3N vector) after superposing conformation 2 onto 1. This is the vector I would like to project onto the first N PCs, so the projections would tell me how much each PCs contribute to the observed conformational change. I guess there is no tool to do that on gromacs (although there are all the ingredients needed), is there ? Thanks, Raul -- View this message in context: http://gromacs.5086.x6.nabble.com/Projecting-conformational-changes-onto-PCs-tp5015560p5015564.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How deuterium order parameters computed?
Hi Everyone,
I have a question about the implementation details of g_order. When I was
reading literatures, I found several interpretations of how the deuterium
order parameters are computed. One is calculate S_{ij} first, then
S_{CD} = \frac{2}{3} S_{xx} + \frac{1}{3} S_{yy}.
Another approach is assuming ideal tetrahedral geometry of the C-D bonds
and the two neighbouring carbons, then reconstruct the coordinates of both
possible Ds, then take the average of the angles between the C-D bonds and
the system normal.
I am curious about that if they are equivalent and which approach was
implemented into GROMACS. It seems the cited paper in g_order.c didn't
mention either of them.
A new order parameter for tetrahedral configurations P.-L. CHAU and A. J.
HARDWICK MOLECULAR PHYSICS, 1998, VOL. 93, NO. 3, 511- 518
Thanks for your clarification.
Bin
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Re: [gmx-users] How deuterium order parameters computed?
I believe the two approaches you list are identical; the prefactors of 2/3
and 1/3 in the equation specified assume a tetrahedral symmetry. This
relation is often just stated as fact (since it is relatively
straightforward to derive) but there is a nice write up of it by J.-P.
Douliez, A. Ferrarini, and E.-J. Dufourc, On the relationship between C-C
and C-D order parameters and its use in studying the conformation of lipid
acyl chains in biomembranes, J. Chem. Phys. 109 (1998).
Also note that this same reference shows the correct derivation of the S_CD
order parameter for sp2 symmetry, which is currently incorrect in Gromacs
has been reported previously (see bug report on redmine:
http://redmine.gromacs.org/issues/1166). There has been some previous
discussion on the list for workarounds for this problem if it applies to
you.
Best,
Reid
On Tue, Apr 1, 2014 at 9:42 PM, Bin Liu fdusuperstr...@gmail.com wrote:
Hi Everyone,
I have a question about the implementation details of g_order. When I was
reading literatures, I found several interpretations of how the deuterium
order parameters are computed. One is calculate S_{ij} first, then
S_{CD} = \frac{2}{3} S_{xx} + \frac{1}{3} S_{yy}.
Another approach is assuming ideal tetrahedral geometry of the C-D bonds
and the two neighbouring carbons, then reconstruct the coordinates of both
possible Ds, then take the average of the angles between the C-D bonds and
the system normal.
I am curious about that if they are equivalent and which approach was
implemented into GROMACS. It seems the cited paper in g_order.c didn't
mention either of them.
A new order parameter for tetrahedral configurations P.-L. CHAU and A. J.
HARDWICK MOLECULAR PHYSICS, 1998, VOL. 93, NO. 3, 511- 518
Thanks for your clarification.
Bin
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send a mail to gmx-users-requ...@gromacs.org.
--
Reid C. Van Lehn
Alfredo Alexander-Katz Research Group
http://soft-materials.scripts.mit.edu/www/member.shtml?member=reid
Ph.D Candidate - Materials Science
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Re: [gmx-users] Flat-bottom potentials
thanks Justin, in the Manual-5.0 i dont see the tool, i am assuming that the .itp file , is generated by a tool similar as genrestr as in older version?? Andrés Ortega -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Flat-bottom potentials
On 4/1/14, 10:37 PM, Andres Ortega Guerrero wrote: thanks Justin, in the Manual-5.0 i dont see the tool, i am assuming that the .itp file , is generated by a tool similar as genrestr as in older version?? There's no separate too; it's just a different function type of the normal [position_restraints] directive. It's in the manual (5.0-beta2 is what I'm looking at), section 4.3.2. Topology specifications are listed with the others in Table 5.5. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] visualize gromacs trajectory in VMD
Hi, This happens due to pbc. You can use trajorder to get right structure. Thanks. On Tue, Apr 1, 2014 at 9:19 PM, sunyeping [via GROMACS] ml-node+s5086n5015551...@n6.nabble.com wrote: Dear all, I am trying to visualize gromacs trajectory in VMD. when I load my .gro file, the GUI window of VMD show a structure that seems to be correct. However, when I load .xtc or .trr file, the strucute shown is seriously deformed. Most bonds become very long and the structures looks very strange. Could anyone tell me how to show the trajectory correctly? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [hidden email]http://user/SendEmail.jtp?type=nodenode=5015551i=0. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/visualize-gromacs-trajectory-in-VMD-tp5015551.html To unsubscribe from GROMACS Users Forum, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4370410code=cHJhdmluazA2OEBnbWFpbC5jb218NDM3MDQxMHwyMDk0ODQ3Njg4 . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- PRAVEEN KUMAR Research scholar INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH PUNE -- View this message in context: http://gromacs.5086.x6.nabble.com/visualize-gromacs-trajectory-in-VMD-tp5015551p5015572.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Projecting conformational changes onto PCs
Hi Raul, The answer to a question with 'projection' and 'eigenvector' is g_anaeig. But you project a structure, not a difference vector. You can also calculate the inner product between two sets of eigenvectors, or between a delta vector and a set of eigenvectors, again using g_anaeig (-inpr). I think that is what you want here. Cheers, Tsjerk On Apr 1, 2014 11:24 PM, rmendez rmen...@email.unc.edu wrote: Hi Tsjerk, Thanks for your answer, but g_anaeig (among other things) gives the projection of each snaphot of my trajectory onto the selected PCs along time. What I want is the projection of a different structure, for instance the difference between my protein into a closed conformation (different from the open conformation that I used in the MD simulations). Ideally I would have a Delta_R vector (3N vector) after superposing conformation 2 onto 1. This is the vector I would like to project onto the first N PCs, so the projections would tell me how much each PCs contribute to the observed conformational change. I guess there is no tool to do that on gromacs (although there are all the ingredients needed), is there ? Thanks, Raul -- View this message in context: http://gromacs.5086.x6.nabble.com/Projecting-conformational-changes-onto-PCs-tp5015560p5015564.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
