[gmx-users] Pulling along dihedral angle as the reaction coordinate
Dear gromacs users, I want to calculate PMF using pull code in gromacs, taking a psi angle as the reaction coordinate. I have a doubt where it is possible with the geometry options, currently available in gromacs? Thanks and regards Neeru -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re:Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology
Dear Justin I thought by use of -pairs I can calculate energy between any 2 groups from index file. when I use g_energy, result is a .xvg file that shows energy of system but I need to calculate energy between specific groups. is there any way for me? thanks Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Aw: Re: [gmx-users] Estimations of the drug's affinity
You can also embed your protein-bound small molecule, protein unbound small molecule a good distance away in solvent of choice, then eq it at the proper temp/pressure. Then take several samples along an equed space, let them just run unrestrained, and you can calculate the energy change mean...same technique as the tutorial munus the pulled aspect. I posted something like this in response to a question Justin answered in a similar way, basically a single value with error estimates is generated, you have an A and B state with no in-between, with no energy curve, ie alot of work but single value. Since I posted this, I realized there are several older 1990s papers that did similar things, and there are large effects on the final affinity from simple solvent changes (salts/ions concentraition, other solvent molecules)... Gesendet:Sonntag, 14. April 2013 um 13:24 Uhr Von:Justin Lemkul jalem...@vt.edu An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] Estimations of the drugs affinity On 4/14/13 2:13 AM, James Starlight wrote: Dear Gromacs users! I wounder to know if it possible to simple estimate drug affinity by mean of MD simulation? As I know the drugs property is based on the free energy change of bound-unbound ligand. So It seems that Justins tutorial (free energy calculations) might be usefull if it would not be so routine for the drugs ( in that workflow several coulombic-vdw interactions must be uncoupled). Is there any more easily way to perform such calculations for the typical small-drug compounds consisted of several non-covalent interactions with the receptors ? Free energy calculations require considerable effort. You can approach the task in a number of ways - FEP, BAR, TI, LIE, PMF, MM/PBSA, etc. There is a large body of literature detailing methods for such calculations. -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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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] g_covar with individual masses
Dear Gromacs users, I want to calculate the covariance matrix of the center of mass coordinates of non standard residues. Since I want to do it mass weighted I need to give the center of mass masses. From which file does g_covar read the masses? Thanks a lot Sebastian -- 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] pbc problem
On 4/14/13 11:21 PM, Kieu Thu Nguyen wrote: Thank Justin ! I used the command editconf -center and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ? Many thanks ! I don't know what it is that you did before, so I can't say. In principle, one could have two leaflets at periodic boundaries along the z-axis and it's exactly the same as having an intact membrane in the center of the box from the standpoint of dynamics. For building membrane protein systems, however, that's less than convenient. -Justin On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul jalem...@vt.edu wrote: On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen kieuthu2...@gmail.com wrote: Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and 0.016000. Maybe your membrane is not centered in the box, but located at the box edge in the z-direction, so that one membrane is distributed over two periodic box images. Another possibility is that your water layer is not thick enough. I think my bilayer stay at between two periodic images. What should i do to put it in corrected position ? It should be a very simple matter of visualization. Use editconf -center to place the membrane wherever you want within the unit cell. You can remove the uncertainty (I think is weak compared to I know) by looking at the box vectors and then numerically determining the center of the membrane with g_traj. That should provide you with all the information you need to determine what's going on. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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 -- 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] binding energy calculation when appear this error: no distance restraints in topology
On 4/15/13 3:01 AM, fatemeh ramezani wrote: Dear Justin I thought by use of -pairs I can calculate energy between any 2 groups from index file. when I use g_energy, result is a .xvg file that shows energy of system but I need to calculate energy between specific groups. is there any way for me? That is not what -pairs does, per the help description. If you want the energy of different components of the system (i.e. residues), you need to set appropriate energygrps in the .mdp file such that short-range nonbonded terms are decomposed. If you did not do this in your simulation, create a new .tpr file with appropriate groups and re-calculate the energies using the original trajectory with mdrun -rerun. Doing so does not decompose long-range terms (i.e. PME). -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] Issue with domain decomposition between v4.5.5 and 4.6.1
On 4/14/13 11:23 PM, Stephanie Teich-McGoldrick wrote: Dear all, I am running a NPT simulation of 33,534 tip4P waters, and I am using domain decomposition as the parallelization scheme. Previously, I had been using Gromacs version 4.5.5 but have recently installed and switched to Gromacs version 4.6.1. Using Gromacs 4.5.5 I can successfully run my water box using domain decomposition over many different processor numbers. However the same simulation returns the following error when I try Gromacs 4.6.1 The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 2.48 nm Y 2.48 nm Z 1.46 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.000 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.40 Y 0.40 Z 0.68 The above error occurred running over 16 nodes / 128 processors. The system runs for version 4.6.1 for 1,8, and 16 processors but not for 32,64, or 128 processors. I have tried other systems (including NVT, Berendsen/PR barostats, anisotropic/isotropic ) at the higher number of processors using both version 4.5.5 and 4.6.1 and get the same result - v4.5.5 runs fine while v4.6.1 returns the error type listed above. Is anyone else having a similar issue? Is there something I am not considering? Any help would be greatly appreciated! The details I have used to compile each code are below. My log files indicate that I am indeed calling the correct executable at run time. Based on what you've posted, I don't see any error. All of the above is normal output. -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] specbond detection
On 4/14/13 11:41 PM, 라지브간디 wrote: Dear gmx, I have mentioned the minimum distance FE bonds to C, O and NE2 (from HIS) in specbond file. As per specbond, the pdb2gmx detect these all bonds and shown in topology file. However, except the FE-C and FE-NE2, i couldn't able to visualize the bonds of FE-O and the bonds between the FE to their pyrrole nitrogen. I looked over the ffbonded.itp file and it looks fine with proper bond angle dihdedral details. What i am missing here? What appears in visualization software is not definitive. The topology is. http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds -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] Pulling along dihedral angle as the reaction coordinate
On 4/15/13 2:27 AM, neeru sharma wrote: Dear gromacs users, I want to calculate PMF using pull code in gromacs, taking a psi angle as the reaction coordinate. I have a doubt where it is possible with the geometry options, currently available in gromacs? This is an application of either dihedral restraints or the new enforced rotation 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
Re: [gmx-users] g_covar with individual masses
On 4/15/13 5:17 AM, Sebastian Waltz wrote: Dear Gromacs users, I want to calculate the covariance matrix of the center of mass coordinates of non standard residues. Since I want to do it mass weighted I need to give the center of mass masses. From which file does g_covar read the masses? The only file g_covar reads that stores mass information is the .tpr file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation
Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I wanted to modify the parameter files of lipids taken from peter teilman site. Taking cue from chris neale (may 2006 gmx mailing list) I changed the c6 and c12 to sigma epsilon using formula Sigma = (c12/c6)^1/6 and epsilon = c6/(4*sigma^6) i tried it for the [pairtypes] in lipid.itp file, but the calculations I made using excel gave me the following: [ pairtypes ] ; i j funct sigma epsilon LO LO 1 1.10E-012.96E-01 LO LOM 1 1.10E-012.96E-0 and so on i.e. the values of sigma and epsilon are interchanged, as opposed to the values listed by chris neale in archive mail (listed below) [ pairtypes ] ; i j funct sigma epsilon LO LO 1 2.96E-011.10E-01 LO LOM 1 2.96E-011.10E-01 LO opls_1161 3.06E-019.47E-02 LO LNL 1 3.10E-019.88E-02 LO LC 1 3.33E-017.76E-02 etc... I am doing something wrong or I can just interchange the values and use them accordingly. Thanking you Parul Tewatia -- 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] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation
On 4/15/13 6:25 AM, Parul tew wrote: Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I wanted to modify the parameter files of lipids taken from peter teilman site. Taking cue from chris neale (may 2006 gmx mailing list) I changed the c6 and c12 to sigma epsilon using formula Sigma = (c12/c6)^1/6 and epsilon = c6/(4*sigma^6) i tried it for the [pairtypes] in lipid.itp file, but the calculations I made using excel gave me the following: [ pairtypes ] ; i j funct sigma epsilon LO LO 1 1.10E-012.96E-01 LO LOM 1 1.10E-012.96E-0 and so on i.e. the values of sigma and epsilon are interchanged, as opposed to the values listed by chris neale in archive mail (listed below) [ pairtypes ] ; i j funct sigma epsilon LO LO 1 2.96E-011.10E-01 LO LOM 1 2.96E-011.10E-01 LO opls_1161 3.06E-019.47E-02 LO LNL 1 3.10E-019.88E-02 LO LC 1 3.33E-017.76E-02 etc... I am doing something wrong or I can just interchange the values and use them accordingly. I think you're doing the calculation wrong, but I can't say exactly how. If I calculate (1.987E-7 / 2.952E-4) ^ (1/6), it comes out to the correct sigma value of 0.29603763. -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] tip5p water model:Atomtype LP1 not found
I have the following files in directory 1.tip5p.gro 2.topol.top 3.em.mdp topol.top: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL 512 commands: editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0 genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro topol.top after genbox command: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Fatal error: No molecules were defined in the system There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I got tip5p.gro from $GMXLIB 1.) editconf -f tip5p.gro -o protein.pdb 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 3 (TIP5P TIP 5-point) 3.) editconf -f protein.gro -o protein-PBC.gro -bt cubic -d 1.0 4.) genbox -cp protein-PBC.gro -cs tip5p.gro -p protein.top -o protein-water.gro 5.) grompp -v -f minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr Fatal error: number of coordinates in coordinate file (protein-water.gro, 37090) does not match topology (protein.top, 34530) What does the [molecules] directive of your .top say? In principle, most of the steps carried out above are unnecessary. You've got pure water, so the topology is easy: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL X ...where X is the number of water molecules. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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 -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
On 4/15/13 6:58 AM, Ahmet yıldırım wrote: I have the following files in directory 1.tip5p.gro 2.topol.top 3.em.mdp topol.top: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL 512 commands: editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0 genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro topol.top after genbox command: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Fatal error: No molecules were defined in the system There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. I cannot reproduce this problem with version 4.6, but it's trivial to just add the correct number of water molecules in the topology by hand. -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] tip5p water model:Atomtype LP1 not found
I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? 2013/4/15 Justin Lemkul jalem...@vt.edu On 4/15/13 6:58 AM, Ahmet yıldırım wrote: I have the following files in directory 1.tip5p.gro 2.topol.top 3.em.mdp topol.top: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] SOL 512 commands: editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0 genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro topol.top after genbox command: #include oplsaa.ff/forcefield.itp #include oplsaa.ff/tip5p.itp [ system ] water [ molecules ] grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Fatal error: No molecules were defined in the system There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. I cannot reproduce this problem with version 4.6, but it's trivial to just add the correct number of water molecules in the topology by hand. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
On 4/15/13 7:22 AM, Ahmet yıldırım wrote: I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? What exactly do you think is wrong? -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] tip5p water model:Atomtype LP1 not found
The norm of force is very high. And the system converged in 3 steps For example, I got the following results for spc water model Steepest Descents converged to Fmax 1000 in 167 steps Potential Energy = -2.1208019e+05 Maximum force = 9.8452704e+02 on atom 286 Norm of force = 4.9830578e+01 2013/4/15 Justin Lemkul jalem...@vt.edu On 4/15/13 7:22 AM, Ahmet yıldırım wrote: I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? What exactly do you think is wrong? -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
On 4/15/13 8:28 AM, Ahmet yıldırım wrote: The norm of force is very high. And the system converged in 3 steps For example, I got the following results for spc water model Steepest Descents converged to Fmax 1000 in 167 steps Potential Energy = -2.1208019e+05 Maximum force = 9.8452704e+02 on atom 286 Norm of force = 4.9830578e+01 Fnorm is not particularly high here or in the previous post. The fact that it converged in 3 steps is also not unexpected. Minimizing a pure water system that is built from pre-equilibrated blocks should be easy. The potential is sensible and the maximum force is below your threshold. Everything is perfectly fine. -Justin 2013/4/15 Justin Lemkul jalem...@vt.edu On 4/15/13 7:22 AM, Ahmet yıldırım wrote: I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? What exactly do you think is wrong? -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Peptide distance matrix
Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? Thank you in advance, Steven -- 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] Peptide distance matrix
On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -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] Peptide distance matrix
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? Steven -- 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] Peptide distance matrix
On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -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] Peptide distance matrix
On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? Steven -- 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] Peptide distance matrix
And another question: I want to analyze all 5 nanoseconds every 20 ns of my trajectory. Would you suggest using trjcat to create one trajectory first and then process to g_mdmat or can I specify time periods (frames) I wish to analyze? Steven On Mon, Apr 15, 2013 at 4:08 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? Steven -- 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] Peptide distance matrix
On 4/15/13 11:17 AM, Steven Neumann wrote: And another question: I want to analyze all 5 nanoseconds every 20 ns of my trajectory. Would you suggest using trjcat to create one trajectory first and then process to g_mdmat or can I specify time periods (frames) I wish to analyze? You have to concatenate whatever intervals you want. Each command only takes one -b and -e flag, not multiple intervals. -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] Peptide distance matrix
On 4/15/13 11:08 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? All C-alpha carbons are in a default index group. Choose it when prompted by g_mdmat and you'll get what you want. -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] Peptide distance matrix
Thank you for this. Steven On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 11:08 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? All C-alpha carbons are in a default index group. Choose it when prompted by g_mdmat and you'll get what you want. -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] Building Single and Double Precision in 4.6.1?
Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- 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] Building Single and Double Precision in 4.6.1?
That's best. GROMACS will take care of a _d suffix for double precision for you. Mark On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote: Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- 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] Peptide distance matrix
And last question: Are these minimum distances averaged over the simulation time? Cannot find any equation the way it is calculated... in Manual its written: This minimum distance between two residues Ai and Aj is defined as the smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output is a symmetrical matrix of smallest distances between all residues. And nothing else... Steven On Mon, Apr 15, 2013 at 4:24 PM, Steven Neumann s.neuman...@gmail.comwrote: Thank you for this. Steven On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 11:08 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? All C-alpha carbons are in a default index group. Choose it when prompted by g_mdmat and you'll get what you want. -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] Peptide distance matrix
On 4/15/13 12:08 PM, Steven Neumann wrote: And last question: Are these minimum distances averaged over the simulation time? Cannot find any equation the way it is calculated... in Manual its written: This minimum distance between two residues Ai and Aj is defined as the smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output is a symmetrical matrix of smallest distances between all residues. And nothing else... The question is answered by reading g_mdmat -h. -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] trjcat set timestep/amb2gmx?
Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? thank you, Steven -- 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] trjcat set timestep/amb2gmx?
On 4/15/13 12:23 PM, Steven Neumann wrote: Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? If you linked against VMD libraries when installing, Gromacs can handle any trajectory/coordinate file format that VMD can, thus requiring no conversion. If you need a .tpr file to do the analysis you are trying to do, then yes, you need to convert topology information into the proper format. -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] Peptide distance matrix
Hey, For the average distance matrix, you can use g_rmsdist. Cheers, Tsjerk On Mon, Apr 15, 2013 at 6:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:08 PM, Steven Neumann wrote: And last question: Are these minimum distances averaged over the simulation time? Cannot find any equation the way it is calculated... in Manual its written: This minimum distance between two residues Ai and Aj is defined as the smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output is a symmetrical matrix of smallest distances between all residues. And nothing else... The question is answered by reading g_mdmat -h. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- 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 enabled gmx 4.5
Dear gmx users, I have installed the mpi (openmpi) enabled gmx4.5.5 version by following command line.It does installed without any errors. However, when i see the folder of installation it doesn't have any files under gromacs except bin (only has mdrun_mpi) and lib folder has lib files. I cant run the gromacs. what is the problem that causing this prob? Used command line ./configure --enable-mpi --enable-float --with-fft=fftw3 --program-suffix=_mpi --prefix=/usr/local/gromacs --enable-float make mdrun make install-mdrun -- 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 enabled gmx 4.5
On 4/15/13 12:43 PM, 라지브간디 wrote: Dear gmx users, I have installed the mpi (openmpi) enabled gmx4.5.5 version by following command line.It does installed without any errors. However, when i see the folder of installation it doesn't have any files under gromacs except bin (only has mdrun_mpi) and lib folder has lib files. I cant run the gromacs. what is the problem that causing this prob? Used command line ./configure --enable-mpi --enable-float --with-fft=fftw3 --program-suffix=_mpi --prefix=/usr/local/gromacs --enable-float make mdrun make install-mdrun You only have mdrun because you only installed mdrun (which is correct, since no other programs are MPI-aware). If you want the rest of the tools, configure without MPI support and proceed with make, then make install. All of these steps are described on the website. -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] muliple GPU crash
I have installed gromacs 4.6.1 on my cluster with dual GTX 670's. The system works well and fast utilizing both GPUs, but as soon as the simulation crashes or i choose to stop it mid-run, my cluster crashes hard needing a manual reboot. I have twice reinstalled it to insure there were no installation errors but the problem persists. Unfortunately i only have one such system to test it on so i am unsure if it is a gromacs error or a cluster specific error(maybe a problem with MPI installation or such). Has anyone else tried more then 1 GPU and come across this problem or does it work fine? Thanks, Brad -- View this message in context: http://gromacs.5086.x6.nabble.com/muliple-GPU-crash-tp5007345.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] why no. of atoms doesn't match?
Hello: I've build a protein/membrane system with CHARMM-GUI, and I am going to use it for Gromacs MD simulation with Slipids FF. First I extract the protein and generate toplogy file by command: pdb2gmx -f protein.pdb -o gmx.pdb -ignh -ter The protein was assigned with Amber FF including TIP3P for solvent after that, I add the following at the top of topol.top file: ; Include forcefield parameters #include slipids.ff/forcefield.itp #include ligand.itp #include popc.itp #include chol.itp and the following at the bottom of topol.top file: [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 CHL1 42 POPC 98 SOL 10079 A the new protein coordinate gmx.pdb was replaced CHEARMM-GUI protein coordinate, all cheloest are put together, all popc were also put together. The order in the complex.pdb are: protein, ligand, cholestrol, popc and water. The system contains 1 protein, 1 ligand, 42 chelostrol, 98 POPC and 10079 water molecules. Then I am trying to minimize the system with command: grompp_mpi -f em.mdp -c complex.pdb -o em.tpr However, it always failed with messages: Program grompp_mpi, VERSION 4.6.1 Source code file: /home/albert/Desktop/gromacs-4.6.1/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (complex.pdb, 49531) does not match topology (topol.top, 51295) I don't understand why Gromacs claim such kind of errors, since to me, everything is all right for my pdb file and toplogy... thank you very much Albert -- 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] switching and shifting in GMX 4.6 on GPUs
Hi Richard, Thanks for the reply. It was very helpful. I've looked at the updated manual regarding the x-modifiers and that cleared it up for me. Best regards, Jesper On Apr 13, 2013, at 4:48 AM, Broadbent, Richard richard.broadben...@imperial.ac.uk wrote: On 12/04/2013 21:50, Jesper Sørensen jesoren...@ucsd.edu wrote: Hi Berk and others, Sorry it has been a long time since this issue was posted, but I got side-tracked from this issue with other projects. And I want to make sure I understand this correctly before venturing into more simulations. So this gets a little long winded, but I hope you will help me figure this out. So following up on the last emails perhaps the nomenclature is not consistent among the programs - which I shoudn't expect it to be either, so that is okay. I know this is the GMX list, but for clarity I will just describe what NAMD does, because it relates to how to run lipids in GMX (particularly with the GPU). NAMD: * When the switching function is on: a smooth switching function will be used to truncate the van der Waals potential energy smoothly at the cutoff distance. * A new vdwForceSwitching method is available as of version 2.7 - which applies a force-based switching function to the VDW term - similar I guess to how CHARMM does it. GMX: * The switch nomenclature is similar/identical to that in NAMD, in that the potential energy is switched off. I can't speak for what NAMD does but this is not what it means in gromacs (or any other MD code I've used). Switched adds a function (which starts at the rcoulomb-switch/rvdw-switch) that smoothly takes both the Energy and the Force to 0 at the cut-off radius. It is the cut-off scheme used to parameterise the force-field I use OPLS-AA and I am certain it was used for many others. It is not supported by the Verlet-cut-off scheme * The shift method in Gromacs is equivalent to the vdwForceSwitching method in NAMD. I doubt it but again I've not used NAMD, shift applies a shift to the Non-bonded potential over its such that the Energy but not the Force goes to 0 at the cut-off, this method does work with the Verlet cut-off scheme and is supported on GPU's. If it is not the method used to parameterise your forcefield, you will have to either perform simulations to check the effect this has on your system and alter your cut-off's accordingly, or find a paper that has done this for you in the literature. And from what Berk was saying earlier and I heard this from Prof. Lindahl during the GPU webinar the other day too, the shift method is the only appropriate option and switching should not be used. It seems that this option is the one used for lipids in NAMD and CHARMM also, so that is great. Now regarding the GPU's you have to run with Verlet groups and here is where it get confusing because looking at the comparison table on the website http://www.gromacs.org/Documentation/Cut-off_schemes; ( I've extracted the important features of this table below). The switched interactions are not available using the Verlet groups and that is okay since that shouldn't be used anyways. But, the shifted interactions are available, but only for the energy - now did we not just agree that when it is the energy that it should be called a switched interaction? Am I missing something here? This is an issue due to you miss understanding the places where these terms are documented very clearly. Non-bonded interaction feature group Verlet exact cut-offshift/switch X cut-off X X shifted interactions force+energyenergy switched interactionsX When I asked Prof. Lindahl during the excellent GPU webinar the other day, he said that switching was implemented and that is sort of what this table says too, but when we try to run a simulation using either switch or shift on the GPU we get the following error: With Verlet lists only cut-off LJ interactions are supported Now I can switch to an exact cut-off method at the cost of making the potential abruptly change to zero at the cut-off - minimizing the abruptness can be achieved by extending the cut-off, but then for the lipids CHARMM, MARTINI, and others, the cut-off seems to be an integral part of the force field development and changing it could prove problematic. So this leaves me to think that lipids simulations shouldn't be run on the GPU as it is currently, at least not without extensive testing. In the 4.6 manual and in the online documentation it explains about new options which are used to control the cut-off scheme see: http://manual.gromacs.org/online/mdp_opt.html#el Using these you can use a shifted cut-off and if necessary for your Force-field correct for the
[gmx-users] Re: why no. of atoms doesn't match?
This error means that your .pdb file contains less then you think it does. Make sure that it has the right number of each kind of molecule(make sure no SOL were accedently deleted). Also another source may be the hydrogen atoms, make sure they were not left out in makint your new .pdb -- View this message in context: http://gromacs.5086.x6.nabble.com/why-no-of-atoms-doesn-t-match-tp5007346p5007348.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] why no. of atoms doesn't match?
On 4/15/13 1:30 PM, Albert wrote: Hello: I've build a protein/membrane system with CHARMM-GUI, and I am going to use it for Gromacs MD simulation with Slipids FF. First I extract the protein and generate toplogy file by command: pdb2gmx -f protein.pdb -o gmx.pdb -ignh -ter The protein was assigned with Amber FF including TIP3P for solvent after that, I add the following at the top of topol.top file: ; Include forcefield parameters #include slipids.ff/forcefield.itp #include ligand.itp #include popc.itp #include chol.itp and the following at the bottom of topol.top file: [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 CHL1 42 POPC 98 SOL 10079 A the new protein coordinate gmx.pdb was replaced CHEARMM-GUI protein coordinate, all cheloest are put together, all popc were also put together. The order in the complex.pdb are: protein, ligand, cholestrol, popc and water. The system contains 1 protein, 1 ligand, 42 chelostrol, 98 POPC and 10079 water molecules. Then I am trying to minimize the system with command: grompp_mpi -f em.mdp -c complex.pdb -o em.tpr However, it always failed with messages: Program grompp_mpi, VERSION 4.6.1 Source code file: /home/albert/Desktop/gromacs-4.6.1/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (complex.pdb, 49531) does not match topology (topol.top, 51295) I don't understand why Gromacs claim such kind of errors, since to me, everything is all right for my pdb file and toplogy... I'll put my money on grompp being right ;) Seriously though, the answer to this question is always the same. You're not counting something right. The solution is something only you can determine. Applying grep -c is your friend here. You're off by 1764 atoms, which may be useful information if any of your molecules are evenly divisible into 1764. Water is, but perhaps other molecules are, as well, depending on their representation. -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] why no. of atoms doesn't match?
Hello Justin and bv08ay: thanks a lot for kind reply. I count each component by isolating them one by one: 1. protein generated by pdb2gmx command: 4739 atoms in all 2. ligand: 79 atoms 3. chelostrol: 74x42= 3108 atoms 4. popc: 116x96= 11368 atoms 5. solvent: 10079x3= 30237 atoms total: 49531 all the above results I double check the no. of coponent and total line (which represent the atom no.) with gedit, the total atoms is 49621. The toplogy give correct no. of each component, and the total no. of such component should be 49621 instead of what claimed by Gromacs does not match topology (topol.top, 51295) It is correct with the topology I defined at the end of topol.top file: [ molecules ] ; Compound#mols Protein 1 LIG1 CHL142 POPC98 SOL10079 thank you very much best Albert On 04/15/2013 07:45 PM, Justin Lemkul wrote: Seriously though, the answer to this question is always the same. You're not counting something right. The solution is something only you can determine. Applying grep -c is your friend here. You're off by 1764 atoms, which may be useful information if any of your molecules are evenly divisible into 1764. Water is, but perhaps other molecules are, as well, depending on their representation. -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] why no. of atoms doesn't match?
Hello: I think I may found the problem: in the popc.itp of Slipid FF, there are 134 atoms defined. However, there are only 116 atoms in the file generated by charmm-GUI. And I found that it is not POPC, but POPA, although I asked for POPC when I proceed online (checked from my cookie). ATOM 6309 P POPA 22 -15.804 13.129 19.464 1.00-18.71 MEMB ATOM 6310 O13 POPA 22 -15.836 12.049 20.465 1.00-18.68 MEMB ATOM 6311 O14 POPA 22 -15.558 14.510 19.908 1.00-18.60 MEMB ATOM 6312 O12 POPA 22 -17.279 13.180 18.915 1.00 0.00 MEMB ATOM 6313 H12 POPA 22 -17.836 13.469 19.643 1.00 0.00 MEMB ATOM 6314 O11 POPA 22 -14.915 12.749 18.217 1.00-17.32 MEMB ATOM 6315 C1 POPA 22 -14.766 13.647 17.113 1.00-16.12 MEMB ATOM 6316 HA POPA 22 -13.736 14.067 17.124 1.00 0.00 MEMB ATOM 6317 HB POPA 22 -15.471 14.513 17.143 1.00 0.00 MEMB ATOM 6318 C2 POPA 22 -14.986 12.875 15.787 1.00-15.10 MEMB ATOM 6319 HS POPA 22 -15.193 11.816 16.082 1.00 0.00 MEMB ATOM 6320 O21 POPA 22 -13.785 12.941 14.994 1.00-14.07 MEMB ATOM 6321 C21 POPA 22 -13.670 11.983 14.087 1.00-13.35 MEMB ATOM 6322 O22 POPA 22 -14.477 11.093 13.884 1.00-13.62 MEMB ATOM 6323 C22 POPA 22 -12.330 12.149 13.368 1.00-12.06 MEMB ATOM 6324 H2R POPA 22 -11.520 12.013 14.114 1.00 0.00 MEMB ATOM 6325 H2S POPA 22 -12.292 13.193 12.997 1.00 0.00 MEMB ATOM 6326 C3 POPA 22 -16.240 13.384 15.014 1.00-14.49 MEMB ATOM 6327 HX POPA 22 -17.103 13.231 15.701 1.00 0.00 MEMB ATOM 6328 HY POPA 22 -16.426 12.735 14.128 1.00 0.00 MEMB ATOM 6329 O31 POPA 22 -16.173 14.793 14.692 1.00-13.57 MEMB ATOM 6330 C31 POPA 22 -15.882 15.097 13.431 1.00-13.15 MEMB ATOM 6331 O32 POPA 22 -15.612 14.299 12.552 1.00-13.67 MEMB ATOM 6332 C32 POPA 22 -15.981 16.618 13.234 1.00-11.81 MEMB ATOM 6333 H2X POPA 22 -14.965 17.021 13.404 1.00 0.00 MEMB ATOM 6334 H2Y POPA 22 -16.629 17.049 14.013 1.00 0.00 MEMB ATOM 6335 C23 POPA 22 -12.145 11.147 12.203 1.00-10.86 MEMB ATOM 6336 H3R POPA 22 -13.002 11.251 11.497 1.00 0.00 MEMB ATOM 6337 H3S POPA 22 -12.165 10.105 12.597 1.00 0.00 MEMB ATOM 6338 C24 POPA 22 -10.842 11.358 11.408 1.00-10.31 MEMB ATOM 6339 H4R POPA 22 -10.828 10.635 10.562 1.00 0.00 MEMB ATOM 6340 H4S POPA 22 -9.965 11.139 12.055 1.00 0.00 MEMB ATOM 6341 C25 POPA 22 -10.721 12.786 10.858 1.00 -8.77 MEMB ATOM 6342 H5R POPA 22 -10.532 13.482 11.706 1.00 0.00 MEMB ATOM 6343 H5S POPA 22 -11.700 13.052 10.409 1.00 0.00 MEMB ATOM 6344 C26 POPA 22 -9.628 13.004 9.802 1.00 -8.20 MEMB ATOM 6345 H6R POPA 22 -8.667 12.568 10.149 1.00 0.00 MEMB ATOM 6346 H6S POPA 22 -9.478 14.104 9.696 1.00 0.00 MEMB ATOM 6347 C27 POPA 22 -9.994 12.452 8.415 1.00 -7.26 MEMB ATOM 6348 H7R POPA 22 -11.033 12.767 8.167 1.00 0.00 MEMB ATOM 6349 H7S POPA 22 -9.974 11.339 8.451 1.00 0.00 MEMB ATOM 6350 C28 POPA 22 -9.039 12.966 7.320 1.00 -6.58 MEMB ATOM 6351 H8R POPA 22 -8.001 12.690 7.614 1.00 0.00 MEMB ATOM 6352 H8S POPA 22 -9.092 14.077 7.305 1.00 0.00 MEMB ATOM 6353 C29 POPA 22 -9.367 12.419 5.955 1.00 -5.84 MEMB ATOM 6354 H91 POPA 22 -10.320 11.873 5.877 1.00 0.00 MEMB ATOM 6355 C210 POPA 22 -8.591 12.542 4.862 1.00 -4.56 MEMB ATOM 6356 H101 POPA 22 -8.934 12.093 3.917 1.00 0.00 MEMB ATOM 6357 C211 POPA 22 -7.259 13.253 4.785 1.00 -3.44 MEMB ATOM 6358 H11R POPA 22 -6.510 12.607 4.276 1.00 0.00 MEMB ATOM 6359 H11S POPA 22 -6.854 13.463 5.801 1.00 0.00 MEMB ATOM 6360 C212 POPA 22 -7.331 14.601 4.034 1.00 -2.53 MEMB ATOM 6361 H12R POPA 22 -6.355 15.121 4.157 1.00 0.00 MEMB ATOM 6362 H12S POPA 22 -8.108 15.238 4.514 1.00 0.00 MEMB ATOM 6363 C213 POPA 22 -7.642 14.470 2.532 1.00 -1.29 MEMB ATOM 6364 H13R POPA 22 -8.457 15.169 2.249 1.00 0.00 MEMB ATOM 6365 H13S POPA 22 -8.008 13.442 2.358 1.00 0.00 MEMB ATOM 6366 C214 POPA 22 -6.441 14.699 1.603 1.00 -0.54 MEMB ATOM 6367 H14R POPA 22 -5.628 13.997 1.898 1.00 0.00 MEMB ATOM 6368 H14S POPA 22 -6.021 15.708 1.737 1.00 0.00 MEMB ATOM 6369 C215 POPA 22 -6.760 14.476 0.116 1.00 0.38 MEMB ATOM 6370 H15R POPA 22
Subject: Re: [gmx-users] Issue with domain decomposition between v4.5.5 and 4.6.1
Hello Justin, Thank you for the reply, and I am glad to hear that this is normal output. Unfortunately, my simulations crash almost immediately when I used v4.6, and I was assuming it has something to do with the load balancing because that is the last line in my md.log file. I have run with the flag mdrun -debug 1 and find the error: mdrun_mpi:13106 terminated with signal 11 at PC=2abd88a03934 SP=7fff6343f170. Backtrace: /apps/x86_64/mpi/openmpi/intel-12.1-2011.7.256/openmpi-1.4.3_oobpr/lib/libmpi.so.0[0x2abd88a03934] I know this is rather vague, but do you have any suggestions on where I should start tracking down this error? When I use particle decomposition my simulations run fine. Thanks in advance! Stephanie Message: 3 Date: Mon, 15 Apr 2013 06:08:13 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Issue with domain decomposition between v4.5.5 and 4.6.1 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 516bd18d.8000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/14/13 11:23 PM, Stephanie Teich-McGoldrick wrote: Dear all, I am running a NPT simulation of 33,534 tip4P waters, and I am using domain decomposition as the parallelization scheme. Previously, I had been using Gromacs version 4.5.5 but have recently installed and switched to Gromacs version 4.6.1. Using Gromacs 4.5.5 I can successfully run my water box using domain decomposition over many different processor numbers. However the same simulation returns the following error when I try Gromacs 4.6.1 The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 2.48 nm Y 2.48 nm Z 1.46 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.000 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.40 Y 0.40 Z 0.68 The above error occurred running over 16 nodes / 128 processors. The system runs for version 4.6.1 for 1,8, and 16 processors but not for 32,64, or 128 processors. I have tried other systems (including NVT, Berendsen/PR barostats, anisotropic/isotropic ) at the higher number of processors using both version 4.5.5 and 4.6.1 and get the same result - v4.5.5 runs fine while v4.6.1 returns the error type listed above. Is anyone else having a similar issue? Is there something I am not considering? Any help would be greatly appreciated! The details I have used to compile each code are below. My log files indicate that I am indeed calling the correct executable at run time. Based on what you've posted, I don't see any error. All of the above is normal output. -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: Subject: Re: [gmx-users] Issue with domain decomposition between v4.5.5 and 4.6.1
On 4/15/13 3:16 PM, Stephanie Teich-McGoldrick wrote: Hello Justin, Thank you for the reply, and I am glad to hear that this is normal output. Unfortunately, my simulations crash almost immediately when I used v4.6, and I was assuming it has something to do with the load balancing because that is the last line in my md.log file. I have run with the flag mdrun -debug 1 and find the error: mdrun_mpi:13106 terminated with signal 11 at PC=2abd88a03934 SP=7fff6343f170. Backtrace: /apps/x86_64/mpi/openmpi/intel-12.1-2011.7.256/openmpi-1.4.3_oobpr/lib/libmpi.so.0[0x2abd88a03934] I know this is rather vague, but do you have any suggestions on where I should start tracking down this error? When I use particle decomposition my simulations run fine. Standard advice applies: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If you want to troubleshoot further, please provide (at minimum) a complete .mdp file. The simple truth is that systems are not infinitely parallelizable, and small changes in number of processors can cause subtle instabilities in the DD algorithm over large numbers of processors. If it worked before, that may have been a random success that now fails. If there is something more nefarious going on, we should be able to weed it out with some careful debugging, but there's no evidence of a bug yet. -Justin Message: 3 Date: Mon, 15 Apr 2013 06:08:13 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Issue with domain decomposition between v4.5.5 and 4.6.1 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 516bd18d.8000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/14/13 11:23 PM, Stephanie Teich-McGoldrick wrote: Dear all, I am running a NPT simulation of 33,534 tip4P waters, and I am using domain decomposition as the parallelization scheme. Previously, I had been using Gromacs version 4.5.5 but have recently installed and switched to Gromacs version 4.6.1. Using Gromacs 4.5.5 I can successfully run my water box using domain decomposition over many different processor numbers. However the same simulation returns the following error when I try Gromacs 4.6.1 The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 2.48 nm Y 2.48 nm Z 1.46 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.000 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.40 Y 0.40 Z 0.68 The above error occurred running over 16 nodes / 128 processors. The system runs for version 4.6.1 for 1,8, and 16 processors but not for 32,64, or 128 processors. I have tried other systems (including NVT, Berendsen/PR barostats, anisotropic/isotropic ) at the higher number of processors using both version 4.5.5 and 4.6.1 and get the same result - v4.5.5 runs fine while v4.6.1 returns the error type listed above. Is anyone else having a similar issue? Is there something I am not considering? Any help would be greatly appreciated! The details I have used to compile each code are below. My log files indicate that I am indeed calling the correct executable at run time. Based on what you've posted, I don't see any error. All of the above is normal output. -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 -- 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] trjcat set timestep/amb2gmx?
On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:23 PM, Steven Neumann wrote: Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? If you linked against VMD libraries when installing, Gromacs can handle any trajectory/coordinate file format that VMD can, thus requiring no conversion. If you need a .tpr file to do the analysis you are trying to do, then yes, you need to convert topology information into the proper format. ...and be aware that a -s option that accepts both .tpr and (say) .gro formats (as shown in g_tool -h) might succeed with the latter if only atom names, rather than (say) bonding connectivity is required for g_tool to work. Mark -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] new CHARMM-GUI output not supported?
Hello: I obtained a POPC lipids from CHARMM-GUI and I found the initial 12 line are following: following atom name order: ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB ATOM 6316 C12 POPC 22 4.563 -22.414 18.821 1.00-17.85 MEMB ATOM 6317 H12A POPC 22 4.337 -21.455 18.379 1.00 0.00 MEMB ATOM 6318 H12B POPC 22 5.583 -22.427 19.173 1.00 0.00 MEMB ATOM 6319 C13 POPC 22 3.979 -23.730 20.844 1.00-17.96 MEMB ATOM 6320 H13A POPC 22 3.969 -24.679 20.329 1.00 0.00 MEMB ATOM 6321 H13B POPC 22 4.977 -23.582 21.229 1.00 0.00 MEMB ATOM 6322 H13C POPC 22 3.420 -23.829 21.763 1.00 0.00 MEMB ATOM 6323 C14 POPC 22 3.424 -21.320 20.778 1.00-20.44 MEMB ATOM 6324 H14A POPC 22 2.552 -21.497 21.391 1.00 0.00 MEMB ATOM 6325 H14B POPC 22 4.281 -21.118 21.404 1.00 0.00 MEMB ATOM 6326 H14C POPC 22 3.249 -20.474 20.130 1.00 0.00 MEMB And here is initial 12 line Slipid popc.itp: ; residue 1 POPC rtp POPC q 0.0 1NTL 1 POPC N 1 -0.6 14.007 ; qtot -0.6 2 CTL2 1 POPCC12 2 -0.1 12.011 ; qtot -0.7 3 CTL5 1 POPCC13 3 -0.35 12.011 ; qtot -1.05 4 CTL5 1 POPCC14 4 -0.35 12.011 ; qtot -1.4 5 CTL5 1 POPCC15 5 -0.35 12.011 ; qtot -1.75 6 HL 1 POPC H12A 6 0.25 1.008 ; qtot -1.5 7 HL 1 POPC H12B 7 0.25 1.008 ; qtot -1.25 8 HL 1 POPC H13A 8 0.25 1.008 ; qtot -1 9 HL 1 POPC H13B 9 0.25 1.008 ; qtot -0.75 10 HL 1 POPC H13C 10 0.25 1.008 ; qtot -0.5 11 HL 1 POPC H14A 11 0.25 1.008 ; qtot -0.25 12 HL 1 POPC H14B 12 0.25 1.008 ; qtot 0 And here is initial 12 line in CHARMM36.ff/lipids.rtp file: [ POPC ] [ atoms ] NNTL-0.600 C12CTL2-0.101 C13CTL5-0.352 C14CTL5-0.353 C15CTL5-0.354 H12AHL0.255 H12BHL0.256 H13AHL0.257 H13BHL0.258 H13CHL0.259 H14AHL0.2510 H14BHL0.2511 As we can see the Slipids popc.itp is the same with CHARMM36.ff/lipids.rtp , but both of which are different from current CHARMM-GUI output. Probably CHARMM-GUI change its format, and Slipids FF and CHARMM36 FF in Gromacs cannot support current new version CHARMM-GUI output? Moreover, the new CHARMM36 FF (both for protein, lipids and ions)introduced Residue pair specific (native contact) non-bonded parameters, nbfix term, probably it is also not supported in current CHARMM36FF in Gromacs? thank you very much best Albert ---BeginMessage--- Hello: I obtained a POPC lipids from CHARMM-GUI and I found the initial 12 line are following: following atom name order: ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB ATOM 6316 C12 POPC 22 4.563 -22.414 18.821 1.00-17.85 MEMB ATOM 6317 H12A POPC 22 4.337 -21.455 18.379 1.00 0.00 MEMB ATOM 6318 H12B POPC 22 5.583 -22.427 19.173 1.00 0.00 MEMB ATOM 6319 C13 POPC 22 3.979 -23.730 20.844 1.00-17.96 MEMB ATOM 6320 H13A POPC 22 3.969 -24.679 20.329 1.00 0.00 MEMB ATOM 6321 H13B POPC 22 4.977 -23.582 21.229 1.00 0.00 MEMB ATOM 6322 H13C POPC 22 3.420 -23.829 21.763 1.00 0.00 MEMB ATOM 6323 C14 POPC 22 3.424 -21.320 20.778 1.00-20.44 MEMB ATOM 6324 H14A POPC 22 2.552 -21.497 21.391 1.00 0.00 MEMB ATOM 6325 H14B POPC 22 4.281 -21.118 21.404 1.00 0.00 MEMB ATOM 6326 H14C POPC 22 3.249 -20.474 20.130 1.00 0.00 MEMB And here is initial 12 line Slipid popc.itp: ; residue 1 POPC rtp POPC q 0.0 1NTL 1 POPC N 1 -0.6 14.007 ; qtot -0.6 2 CTL2 1 POPCC12 2 -0.1 12.011 ; qtot -0.7 3 CTL5 1 POPCC13 3 -0.35 12.011 ; qtot -1.05 4 CTL5 1 POPCC14 4 -0.35 12.011 ; qtot -1.4 5 CTL5 1 POPCC15 5 -0.35 12.011 ; qtot -1.75 6 HL 1 POPC H12A 6 0.25 1.008 ; qtot -1.5 7 HL 1 POPC H12B 7 0.25 1.008 ; qtot -1.25 8 HL 1 POPC H13A 8 0.25 1.008 ; qtot -1 9 HL 1 POPC H13B 9 0.25 1.008 ; qtot -0.75 10 HL 1 POPC H13C 10 0.25 1.008 ; qtot -0.5 11 HL 1 POPC H14A 11
[gmx-users] Pulling along dihedral angle as the reaction coordinate
I came across one such application name PLUMED plugin for gromacs, for dihedral restraints as the reaction coordinate. If you can suggest any other application for the same, kindly let me know. --Thanks Neeru On 4/15/13 2:27 AM, neeru sharma wrote: Dear gromacs users, I want to calculate PMF using pull code in gromacs, taking a psi angle as the reaction coordinate. I have a doubt where it is possible with the geometry options, currently available in gromacs? This is an application of either dihedral restraints or the new enforced rotation options. -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
