[gmx-users] Re:qmmm temp definition + linking atom
The link atom can be placed anywhere at step 0. These atom are treated like virtual sites and will thus be placed at the defined position along the QM/MM bond that needs capping. Concerning the temperature, one can treat the QM atoms as a separate group indeed. But as Mark said, why not expose the whole system to the temp-shock? Gerrit 4. qmmm temp definition (Yao Yao) 5. qmmm linking atom (Yao Yao) 6. Re: qmmm temp definition (Mark Abraham) -- 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] Running md in different systems
Dear users, I was running an MD in a system with 8 cores, for some reasons I had to shift the job to another system with same OS and gromacs version. After I started runnning it said Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. How does this effect the run and also it gave a warning saying WARNING: This run will generate roughly 2054591408127343104 Mb of data !! which generally used to be around 5GB! What is wrong here? Thank you With regards Kavya -- 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_current and output redirection
Hello Vitaly, the intention to write out informations to the stdout and the stderr was that you have the ability to sort it during the analysis. However as Justin mentionen will write all open pipes into one file. Cheers, Flo On Tue, 2011-05-10 at 13:16 -0400, Vitaly Chaban wrote: Thanks, Justin! Great solution. On Tue, May 10, 2011 at 12:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vitaly Chaban wrote: I have a pure linux question. When using g_current and trying to redirect its output to the file, e.g. g_current -temp $TEMPER -b $conduct_b -e $conduct_e EOF output 0 EOF only a part of output is written to the file (output) Here is what is actually written to the file: Selected 0: 'System' Average translational dipole moment M_J [enm] after 25001 frames (|M|^2): 5.554790 -5.833042 -0.539783 (68.255722) Average molecular dipole moment M_D [enm] after 25001 frames (|M|^2): -0.414639 -0.356325 0.148187 (2.359227) Thus, the relevant data (sigma, dielectric constant) are missed. My question is how to redirect all the output of g_current to my file. echo 0 | g_current (options) outfile -Justin Thanks! Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] Continuing job in another machine
Dear users, I was running an MD in a machine with 2 quad core processors using all 8 cores system cores, for some reasons I had to shift the job to another machine with 2 quad cores processors, identical OS and gromacs version using 8 cores. After I started runnning using check point file it said - Build time mismatch, current program: Thu Jan 20 12:00:01 IST 2011 checkpoint file: Thu Jan 20 11:57:38 IST 2011 Build user mismatch, current program: kavya@alder checkpoint file: kavya@yamuna Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. How does this effect the run and also it gave a warning saying WARNING: This run will generate roughly 2054591408127343104 Mb of data !! which generally used to be around 5GB! What is wrong here? Kindly reply. Thank you With regards Kavya -- 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] Continuing job in another machine
On 11/05/11, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was running an MD in a machine with 2 quad core processors using all 8 cores system cores, for some reasons I had to shift the job to another machine with 2 quad cores processors, identical OS and gromacs version using 8 cores. After I started runnning using check point file it said - Build time mismatch, current program: Thu Jan 20 12:00:01 IST 2011 checkpoint file: Thu Jan 20 11:57:38 IST 2011 Build user mismatch, current program: kavya@alder checkpoint file: kavya@yamuna Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. How does this effect the run and also it gave a warning saying See http://www.gromacs.org/Documentation/Terminology/Reproducibility. Under normal circumstances there is nothing of concern. WARNING: This run will generate roughly 2054591408127343104 Mb of data !! which generally used to be around 5GB! What is wrong here? Kindly reply. Some kind of integer datatype is different on the two machines, and some kind of overflow is happening in the estimation. Don't worry about it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Continuing job in another machine
Respected Sir, So that number doesnt mean what it says! Thanking you With regards kavya On Wed, May 11, 2011 at 4:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/05/11, *Kavyashree M * hmkv...@gmail.com wrote: Dear users, I was running an MD in a machine with 2 quad core processors using all 8 cores system cores, for some reasons I had to shift the job to another machine with 2 quad cores processors, identical OS and gromacs version using 8 cores. After I started runnning using check point file it said - Build time mismatch, current program: Thu Jan 20 12:00:01 IST 2011 checkpoint file: Thu Jan 20 11:57:38 IST 2011 Build user mismatch, current program: kavya@alder checkpoint file: kavya@yamuna Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. How does this effect the run and also it gave a warning saying See http://www.gromacs.org/Documentation/Terminology/Reproducibility. Under normal circumstances there is nothing of concern. WARNING: This run will generate roughly 2054591408127343104 Mb of data !! which generally used to be around 5GB! What is wrong here? Kindly reply. Some kind of integer datatype is different on the two machines, and some kind of overflow is happening in the estimation. Don't worry about it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Surface area calculation
Can anyone explain in detail the method that gromacs uses to calculate surface area? Which surface area is it calculating (e.g., connolley, accessible)? I am under the impression that the final result is given in nm^2. Is this correct? Carrying out the surface area calculation in gromacs using the OPLS all atom force field I obtain a value of 4.43 nm^2 for methane (carbon = opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC ideal bond length = 0.109, e=284512). The command was g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc and the result was taken from resarea.xvg I have written a program to calculate the geometric accessible surface area using the van der waals radius of the atoms and a probe of a given size. The surface is defined from the centre of the probe. Using the above values for sigma I obtain a value for methane of 1.15 nm^2 with a probe diameter of 0.2 nm. Obviously the two do not match and I am not sure why. The individual atom areas for my molecule are: C 0.22 H 0.24 H 0.23 H 0.22 H 0.24 Attached are the files used in the gromacs calculation along with the output and my own program. If any one has any suggestions please let me know. # This file was created Wed May 11 13:05:56 2011 # by the following command: # g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc # # g_sas is part of G R O M A C S: # # Gravel Rubs Often Many Awfully Cauterized Sores # @title Solvent Accessible Surface @xaxis label Time (ps) @yaxis label Area (nm\S2\N) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrophobic @ s1 legend Hydrophilic @ s2 legend Total @ s3 legend D Gsolv 0 4.43467 0 4.43467-11.1328 # This file was created Wed May 11 13:05:56 2011 # by the following command: # g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc # # g_sas is part of G R O M A C S: # # Gravel Rubs Often Many Awfully Cauterized Sores # @title Area per atom @xaxis label Atom # @yaxis label Area (nm\S2\N) @TYPE xy 1 1.53938 0.000291734 2 0.723823 0 3 0.723823 0 4 0.723823 0 5 0.723823 0 methane 5 1DRGCT1 0.000 0.000 0.000 1DRGHC2 0.000 0.000 1.089 1DRGHC3 1.027 0.000 -0.363 1DRGHC4 -0.513 -0.889 -0.363 1DRGHC5 -0.513 0.889 -0.363 7.90500 7.90500 7.90500 ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1000 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 50 nstenergy= 50 ; Output frequency and precision for xtc file nstxtcout= 50 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric
Re: [gmx-users] REMD: after replica exchange breakdown
On 05/11/2011 05:20 AM, Mark Abraham wrote: On 05/11/2011 02:32 AM, SebastianWaltz wrote: Dear GROMACS User, I'm running a REMD MD of 32 replicas. It worked for the first few replica exchanges. After 30ps again two replicas were exchanged and I received the Error: x particles communicated to PME node y are more than a cell length out of the domain decomposition cell of their charge group The only rationale I can see is that a velocity was scaled after exchange that was now large enough to lead to the normal sort of exploding system. Was the exploding replica going up in temperature? How did you equilibrate the systems? I did a NPT equilibration for each replica which leads obviously to different volumes and looks like to cause some problems. If I use the same volume for each replica it works fine. I am using NVT assembles for each replica with a exchanging interval of 5ps. For each replica I use 4 processors. Constraint are only the bonds to hydrogens (constraints = hbonds). Using PME for electro static. Information like GROMACS version, simulation system dimensions and contents would be useful. What replica temperature distribution exists? I am using version 4.0.7. My system consists of a small peptide soluted in ~1500 rigid CHCl3 molecules. System equilibrated with NPT and NVT production run seems to work only if I increase the number of replicas (32-64) meaning that I also decrease the difference of the volumes. The temperature is exponentially distributed from 200 to 450K. When running each replica for its own everything is working fine, nothing is blowing up like one would expect after getting the above Error. Good trouble-shooting :) You'd have been told to try this otherwise... Mark 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] Surface area calculation
reference: Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M (1995) J. Comput. Chem. 16, 273-284. On May 11, 2011, at 2:34 PM, Laura Leay wrote: Can anyone explain in detail the method that gromacs uses to calculate surface area? Which surface area is it calculating (e.g., connolley, accessible)? I am under the impression that the final result is given in nm^2. Is this correct? Carrying out the surface area calculation in gromacs using the OPLS all atom force field I obtain a value of 4.43 nm^2 for methane (carbon = opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC ideal bond length = 0.109, e=284512). The command was g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 - nopbc and the result was taken from resarea.xvg I have written a program to calculate the geometric accessible surface area using the van der waals radius of the atoms and a probe of a given size. The surface is defined from the centre of the probe. Using the above values for sigma I obtain a value for methane of 1.15 nm^2 with a probe diameter of 0.2 nm. Obviously the two do not match and I am not sure why. The individual atom areas for my molecule are: C 0.22 H 0.24 H 0.23 H 0.22 H 0.24 Attached are the files used in the gromacs calculation along with the output and my own program. If any one has any suggestions please let me know. area .xvg atomarea .xvg conf .gro grompp.mdpmethane.itpresarea.xvgtopol.topPIsurfaceOPLS.f90-- 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] Surface area calculation
Laura Leay skrev 2011-05-11 14.34: Can anyone explain in detail the method that gromacs uses to calculate surface area? Which surface area is it calculating (e.g., connolley, accessible)? I am under the impression that the final result is given in nm^2. Is this correct? Carrying out the surface area calculation in gromacs using the OPLS all atom force field I obtain a value of 4.43 nm^2 for methane (carbon = opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC ideal bond length = 0.109, e=284512). The command was g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc and the result was taken from resarea.xvg I have written a program to calculate the geometric accessible surface area using the van der waals radius of the atoms and a probe of a given size. The surface is defined from the centre of the probe. Using the above values for sigma I obtain a value for methane of 1.15 nm^2 with a probe diameter of 0.2 nm. One difference is that g_sas -probe 0.2 uses a probe with a 0.2 nm *radius*, while your code use a 0.2 nm diameter. That doesn't on its own explain the difference you report, but you probably want to use the same probe when comparing. Erik Obviously the two do not match and I am not sure why. The individual atom areas for my molecule are: C 0.22 H 0.24 H 0.23 H 0.22 H 0.24 Attached are the files used in the gromacs calculation along with the output and my own program. If any one has any suggestions please let me know. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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] reg pushing rate
Dear justin thank you for your mail to push a mobile group towards reference group I set the pull_rate in negative value (-0.1) as u said My question is when i change the pull rate to less negative value (-0.01) will push rate increases or decreases? because my doubt is about sign .it means if set pull rate to high negative value will push rate decrases or increase sign confuse me i am expcting valuable reply Thanks in Advance -- 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] reg pushing rate
vidhya sankar wrote: Dear justin thank you for your mail to push a mobile group towards reference group I set the pull_rate in negative value (-0.1) as u said My question is when i change the pull rate to less negative value (-0.01) will push rate increases or decreases? because my doubt is about sign .it means if set pull rate to high negative value will push rate decrases or increase sign confuse me i am You can answer this question yourself with a simple test. As stated in the manual, pull_rate is the rate of change in the position of the pulled group. -Justin expcting valuable reply Thanks in Advance -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about g_hbond
Hi, For group A, b, C. It's no doubt can get hb forming number between A-b, b-C. b-(A or C). But I don't know how to get the number of residues of b forming both with A and B at the same time. namely b-AC, not with AC group. Thanks, -- Best Regards, lina -- Best Regards, lina -- 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] about g_hbond
lina wrote: Hi, For group A, b, C. It's no doubt can get hb forming number between A-b, b-C. b-(A or C). But I don't know how to get the number of residues of b forming both with A and B at the same time. namely b-AC, not with AC group. There's no direct way to do it, but from the output files of g_hbond it can be done. You'd need the .xpm files of A-C and B-C hydrogen bonds, and write some script that parses the .xpm files, and whenever there is an entry of A-C in the same frame as B-C, then you have a hydrogen bond mediated between the two. There's lots of discussion in the list archive about water-mediated hydrogen bonds that is likely applicable here. Note that if you're using g_hbond in version 4.5, there is an important bug that was fixed just yesterday: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html -Justin Thanks, -- Best Regards, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tabulated potential energy=nan for r=0 nm and charged atoms
Dear users: with assistance from Berk on the developers list, I am posting a work-around to this issue. the nonbonded interactions calculate the nonbonded distance, r, using the gmx_invsqrt function. Thus, the optimized kernel from 4.5.4 and 4.0.7 both give nan when two charges occupy the space, even when using tables that specify the force and potential energy to be zero. I had expected that I would need to modify the generic kernel source, but that turned out to be unnecessary -- just using it was enough. For some reason, using export GMX_NOOPTIMIZEDKERNELS=1 prior to running mdrun solves the issue for 4.5.4 but not 4.0.7 (on my architecture). To solve the problem in v4.0.7 (and this also works for v4.5.4) I must export GMX_NB_GENERIC=1; export GMX_NO_SOLV_OPT=1 prior to running mdrun. Note that the generic nonbonded kernel runs 1.1x slower then the unoptimized kernel, which itself runs 2.4x slower than the optimized kernel (on my architecture for this system). Thank you, Chris. -- original message -- Dear Users: I am trying to work with tabulated potentials for the first time. I would like to allow 2 charges to be at the same spot. Imagine taking a sodium and chloride ion and removing the LJ entirely and I want the system to evaluate energies correctly and be stable during the simulation. It was my intention to add a sort-of soft-core to the charge-charge interactions at very close distances so that the system did not crash. However, my testing didn't even get that far. I find that the Coulomb(SR) energy = nan even when using tables that suggest it should be zero. I suppose that there is some other place in the code where this problem develops? While looking at share/gromacs/top/table6-12.xvg it seems that this should not lead to energies of nan, but it does. $ head share/gromacs/top/table6-9.xvg # # Table AB1: ndisp=6 nrep=9 # 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 2.00e-03 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 4.00e-03 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 6.00e-03 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 8.00e-03 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 1.00e-02 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 1.20e-02 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 and therefore, according to manual 4.5.4 page 151 equation 6.23, the [(qi*qj)/(4*pi*epsilon)]*f(rij) coulomb SR value should equal zero. I tried a few things, like modifying the values so that they are constant from 0 to 0.04 nm in the table.xvg file, but this did not help. here is the .top file that I used along with ffoplsaa to test out this idea: #include ffoplsaa.itp #include na.itp [ system ] ; name tables [ molecules ] ; name number MOL_A 1 MOL_B 1 and here is the .itp file that I used along with ffoplsaa to test out this idea: [ atomtypes ] aaa AA 8 15.999400.0 A0.0 0.0 [ moleculetype ] ; molname nrexcl MOL_A 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 aaa 1 MLA AA 11.0 [ moleculetype ] ; molname nrexcl MOL_B 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 aaa 1 MLB BB 1-1.0 And the .gro file: title 2 1MLA AA1 0.000 0.000 0.000 1MLB BB1 0.000 0.000 0.000 5.0 5.0 5.0 ### And my .mdp file is nsteps = 0 ns_type = grid rlist = 1 rcoulomb = 1 rvdw = 1 coulombtype = user tc_grps = System tau_t = 1.0 ld_seed = -1 ref_t = 300 gen_temp = 300 gen_vel = yes unconstrained_start = no gen_seed = -1 Pcoupl = berendsen pcoupltype = isotropic tau_p = 4 compressibility = 4.5e-5 ref_p = 1.0 Still, when I run a 0-step mdrun (mdrun -deffnm md1 -table mod2.table.xvg), I get: Energies (kJ/mol) LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 0.0e+00nannannannan Temperature Pressure (bar) nannan # I get the same thing if the two charges are like or dislike... But if I then modity my topologies to turn the +1 charge to zero, I get sensible output:
[gmx-users] exclusions
Hi all
I am cheking the non binary version topol.tpr form grompp and I was
wondering what the following format for the exclusion section signifies?
excls:
nr=228
nra=1920
excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16}
excls[1][13..25]={0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 15}
Also I take it, that this is a result of nrexcl =3
Cheers
Gavin
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[gmx-users] Rigid structure and flexible structure present in sing system
Hi, For a while I've been looking for a way to include a rigid (macromolecular) structure and a flexible (small-protein) structure in a single system and have not had much success. I looked for a way to apply a different set of constraints to each structure, but couldn't find one. I looked into modifying the topology file, but the only method I could find was to artificially increase the mass of every atom in the rigid structure and this does not save any computing time. Does anyone know how I can fix the relative co-ordinates of one structure and only calculate the MD of another? Any constructive criticism (even if to inform me that I'm doing something ridiculous) is very gratefully received. Kind regards, Luke -- 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] exclusions
Regarding my earlier post- If someone could confirm.
Taking into account that atom indices start from zero.
Then excls[0] = exclusions centred around atom 1.
[0..12] = there are 13 exclusions each one labelled form 0-12.
I then assume that you read the exclusions with respect to atom 0
(actual index =1)
In the next set do you read the exclusion with respect to atom 1 (actual
index =2).
and so on
Many thanks in advance
Gavin
Gavin Melaugh wrote:
Hi all
I am cheking the non binary version topol.tpr form grompp and I was
wondering what the following format for the exclusion section signifies?
excls:
nr=228
nra=1920
excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16}
excls[1][13..25]={0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 15}
Also I take it, that this is a result of nrexcl =3
Cheers
Gavin
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[gmx-users] Rigid structure and flexible structure present in sing system
If I read between the lines correctly, you know how to do this in gromacs, but you wish that you got a big speedup from freezing most of the atoms in your system. If that is the case, then I think that gromacs can not help you in its current form. Therefore, I suggest that you try the Charmm software. It may be slower overall, but it gives you the speedup you expect when you freeze 95% of the atoms in your system so it may be much faster for your usage. Other software may also do this, but I have no experience with it. If you have explicit water, this won't be of much use since you're still only freezing 10% of the atoms in your system. If you simply want to know how to freeze one structure, then use freeze groups and energy exclusions without pressure coupling, or use position restraints and refcoordscaling=com with position restraints, or create an elastic network of restraints. Chris. -- original message -- Hi, For a while I've been looking for a way to include a rigid (macromolecular) structure and a flexible (small-protein) structure in a single system and have not had much success. I looked for a way to apply a different set of constraints to each structure, but couldn't find one. I looked into modifying the topology file, but the only method I could find was to artificially increase the mass of every atom in the rigid structure and this does not save any computing time. Does anyone know how I can fix the relative co-ordinates of one structure and only calculate the MD of another? Any constructive criticism (even if to inform me that I'm doing something ridiculous) is very gratefully received. Kind regards, Luke -- 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] Rigid structure and flexible structure present in sing system
Luke Goodsell wrote: Hi, For a while I've been looking for a way to include a rigid (macromolecular) structure and a flexible (small-protein) structure in a single system and have not had much success. I looked for a way to apply a different set of constraints to each structure, but couldn't find one. I looked into modifying the topology file, but the only method I could find was to artificially increase the mass of every atom in the rigid structure and this does not save any computing time. Add a [constraints] directive for the molecule you want to make rigid and use constraints = none in the .mdp file. Thus, only the bonds manually set to be constraints will be constrained. Note that by constraining one molecule but not another, you still can't save any computing time, because the timestep of the simulation will still be limited by any bonds that are still harmonic (especially X-H). Your system probably won't be stable with dt 1 fs, even with some molecule(s) constrained. Does anyone know how I can fix the relative co-ordinates of one structure and only calculate the MD of another? Any constructive criticism (even if to inform me that I'm doing something ridiculous) is very gratefully received. I don't see any value in constraining one molecule but not another. You can't increase the timestep and you lose the ability to have rigid bonds. The argument can be made that a rigid bond is a better representation of reality than a harmonic one for most biological applications, or any done at ambient temperature, really. -Justin Kind regards, Luke -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] selecting groups for full trajectory
Hello, I wish to select the groups for full precision trajectory (.trr files). Is there a way to choose which group should be written to trr files (like xtc-groups for .xtc files). Since I need the forces and velocities, xtc trajectory won't work. Thanks in advance, Ravi Bhadauria -- 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] selecting groups for full trajectory
Ravi Bhadauria wrote: Hello, I wish to select the groups for full precision trajectory (.trr files). Is there a way to choose which group should be written to trr files (like xtc-groups for .xtc files). Since I need the forces and velocities, xtc trajectory won't work. There is no equivalent option. You can extract forces and velocities after the simulation using g_traj and any index group of your choosing. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CG database for POPC
have written a program to calculate the geometric accessible surface area using the van der waals radius of the atoms and a probe of a given size. The surface is defined from the centre of the probe. Using the above values for sigma I obtain a value for methane of 1.15 nm^2 with a probe diameter of 0.2 nm. Obviously the two do not match and I am not sure why. The individual atom areas for my molecule are: C 0.22 H 0.24 H 0.23 H 0.22 H 0.24 Attached are the files used in the gromacs calculation along with the output and my own program. If any one has any suggestions please let me know. area .xvg atomarea .xvg conf .gro grompp.mdpmethane.itpresarea.xvgtopol.topPIsurfaceOPLS.f90-- 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 -- Message: 3 Date: Wed, 11 May 2011 15:48:36 +0200 From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] Surface area calculation To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dca93b4.3030...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed Laura Leay skrev 2011-05-11 14.34: Can anyone explain in detail the method that gromacs uses to calculate surface area? Which surface area is it calculating (e.g., connolley, accessible)? I am under the impression that the final result is given in nm^2. Is this correct? Carrying out the surface area calculation in gromacs using the OPLS all atom force field I obtain a value of 4.43 nm^2 for methane (carbon = opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC ideal bond length = 0.109, e=284512). The command was g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc and the result was taken from resarea.xvg I have written a program to calculate the geometric accessible surface area using the van der waals radius of the atoms and a probe of a given size. The surface is defined from the centre of the probe. Using the above values for sigma I obtain a value for methane of 1.15 nm^2 with a probe diameter of 0.2 nm. One difference is that g_sas -probe 0.2 uses a probe with a 0.2 nm *radius*, while your code use a 0.2 nm diameter. That doesn't on its own explain the difference you report, but you probably want to use the same probe when comparing. Erik Obviously the two do not match and I am not sure why. The individual atom areas for my molecule are: C 0.22 H 0.24 H 0.23 H 0.22 H 0.24 Attached are the files used in the gromacs calculation along with the output and my own program. If any one has any suggestions please let me know. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- Message: 4 Date: Wed, 11 May 2011 20:15:20 +0530 (IST) From: vidhya sankar scvsankar_...@yahoo.com Subject: [gmx-users] reg pushing rate To: gmx-users@gromacs.org Message-ID: 214557.84456...@web95502.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear justin thank you for your mail ??? to push a mobile group towards reference group? I set the pull_rate in negative value (-0.1) as u said My question is ?when i change the pull rate to less negative value (-0.01) will push rate increases or decreases? ?because my doubt is about sign .it means if set pull rate to high negative value will push rate decrases or increase sign confuse me? i am expcting? valuable reply Thanks in Advance -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110511/0e9443c4/attachment-0001.html -- Message: 5 Date: Wed, 11 May 2011 10:47:59 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] reg pushing rate To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dcaa19f.1000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed vidhya sankar wrote: Dear justin thank you for your mail to push a mobile group towards reference group I set the pull_rate in negative value (-0.1) as u said My question is when i change the pull rate to less negative value (-0.01) will push rate increases or decreases? because my doubt is about sign .it means if set pull rate to high negative value will push rate decrases or increase sign confuse me i am You can answer this question yourself with a simple test
Re: [gmx-users] CG database for POPC
Du Jiangfeng (BIOCH) wrote: Dear All, I require a CG database of POPC for coarse grained simulation. Can anyone give some suggestions for where to find it or how to make it by myself? PS: the structure file of POPC was from the Biocomputing, Department of Biological Sciences, University of Calgary. Thank you in advance. The MARTINI site has a variety of coordinate and topology files you can likely make use of: http://md.chem.rug.nl/cgmartini/index.php/downloads I don't believe they have a pure POPC membrane, but they do have POPE, which can easily be converted. In the future, please do not respond to the entire digest, especially when starting a new and entirely unrelated thread. It confuses the archive horribly. It's bad enough, let's not make it any worse :) -Justin Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Genbox question
Hello, I was wondering if someone can help me with a general genbox question. I have been using the command line: genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro to fill a box with 1000 molecules of octanol. With the smaller n-alcohols, it worked fine but as I started using 1-butanol, 1-pentanol, (longer carbon chains) up to octanol, Gromacs sometimes ends the command with a 'Killedin-Solvent overlap' line at the very end. Sometimes increasing the box size helped, but for 1-pentanol, even 7 7 7 box size didn't work. Also, do these killed runs take up some sort of space. My memory space decreases a little bit even on failed runs. Thanks. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.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] Genbox question
Fabian Casteblanco wrote: Hello, I was wondering if someone can help me with a general genbox question. I have been using the command line: genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro to fill a box with 1000 molecules of octanol. With the smaller n-alcohols, it worked fine but as I started using 1-butanol, 1-pentanol, (longer carbon chains) up to octanol, Gromacs sometimes ends the command with a 'Killedin-Solvent overlap' line at the very end. Sometimes increasing the box size helped, but for 1-pentanol, even 7 7 7 box size didn't work. Also, do these killed runs take up some sort of space. My memory space decreases a little bit even on failed runs. Generating random boxes in this way requires lots of memory and is prone to failure. A useful strategy is to overestimate the size of the box so that genbox doesn't have to do too many iterations to place all of the molecules, then run a nice, long equilibration to get the box vectors (and therefore density, etc) correct. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Genbox question
Justin A. Lemkul wrote: Fabian Casteblanco wrote: Hello, I was wondering if someone can help me with a general genbox question. I have been using the command line: genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro to fill a box with 1000 molecules of octanol. With the smaller n-alcohols, it worked fine but as I started using 1-butanol, 1-pentanol, (longer carbon chains) up to octanol, Gromacs sometimes ends the command with a 'Killedin-Solvent overlap' line at the very end. Sometimes increasing the box size helped, but for 1-pentanol, even 7 7 7 box size didn't work. Also, do these killed runs take up some sort of space. My memory space decreases a little bit even on failed runs. Generating random boxes in this way requires lots of memory and is prone to failure. A useful strategy is to overestimate the size of the box so that genbox doesn't have to do too many iterations to place all of the molecules, then run a nice, long equilibration to get the box vectors (and therefore density, etc) correct. A more reliable method is probably genconf: genconf -f molecule.gro -nbox 10 10 10 -o box.gro You'll get 1000 molecules every time and the box size should be sensible. Then proceed with equilibration. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_current and output redirection
Hi Flo, Do you imply that conductivity and dielectric constant from g_current go to the error stream? But why, if these are not errors Vitaly On Wed, May 11, 2011 at 5:07 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: Hello Vitaly, the intention to write out informations to the stdout and the stderr was that you have the ability to sort it during the analysis. However as Justin mentionen will write all open pipes into one file. Cheers, Flo On Tue, 2011-05-10 at 13:16 -0400, Vitaly Chaban wrote: Thanks, Justin! Great solution. On Tue, May 10, 2011 at 12:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vitaly Chaban wrote: I have a pure linux question. When using g_current and trying to redirect its output to the file, e.g. g_current -temp $TEMPER -b $conduct_b -e $conduct_e EOF output 0 EOF only a part of output is written to the file (output) Here is what is actually written to the file: Selected 0: 'System' Average translational dipole moment M_J [enm] after 25001 frames (|M|^2): 5.554790 -5.833042 -0.539783 (68.255722) Average molecular dipole moment M_D [enm] after 25001 frames (|M|^2): -0.414639 -0.356325 0.148187 (2.359227) Thus, the relevant data (sigma, dielectric constant) are missed. My question is how to redirect all the output of g_current to my file. echo 0 | g_current (options) outfile -Justin Thanks! Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to freeze groups
Hello, Can anyone suggest some tutorials or sample top files for simulations involving freezing of groups? I dont see much info in chapter 5 of manual. Thanks, -- 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] How to freeze groups
Elisabeth wrote: Hello, Can anyone suggest some tutorials or sample top files for simulations involving freezing of groups? I dont see much info in chapter 5 of manual. You're looking in the wrong place - freezing is not handled in the topology. Use the freezegrps .mdp keyword with a group of your choice. The group may require a custom index group if it is one of the non-standard ones. Try manual section 7.3.24. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: [gmx-developers] flexible water model
Hello Justin, I used 0.5 fs time step and still I got dielectric constant ~2. This is the md.mdp file I used. I checked the temperature it didn't go more than ~ 320 K. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 650 ; total 5 ps. nstcomm = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1 nstlist = 1 ns_type = grid rlist = 0.6 rcoulomb= 0.6 rvdw= 0.7 coulombtype = PME vdwtype = cut-off pbc = xyz 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 = v-rescale tau_t = 0.1 tc-grps =system ref_t = 295 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 295.0 gen_seed= 173529 Nilesh On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote: The gmx-developers list is not the forum for these types of questions. I am replying via gmx-users, which is where the discussion should stay. I took a few minutes to dig into this. My conclusion is that your system is not stable. I would encourage you to analyze the temperature and pressure of your systems that are giving odd results. When I used the topology you provided, the temperature spiked to over 600 K and the box began to oscillate extensively as if the system were about to explode. The resulting epsilon value was about 1.6. If I reduce the timestep to 0.5 fs, the results are much more reasonable, and using the Ka and Kb values in the paper (not halved!) I get a much more sensible result, even after just 100 ps. It looks to me as if the combination of these parameters and a 1-fs timestep is not entirely stable. I know the original authors used dt = 1 fs, but the point remains. -Justin Nilesh Dhumal wrote: Hello, I am using flexible water model for my system. I am referring a paper J. Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. Kbond = 443153.3808 kJ/mol nm**2 Kangle= 317.5656 kJ/mol rad**2. I am using olss-aa force field parameters in Gromacs VERSION 4.0.7. I checked some papers in which author have used oplsaa force field in Gromacs. 1/2 factor is not in opls force field if I compare opls and amber. I didnt get the proper dielectric constant for water when I used the parameters reported in paper (Kbond = 443153.3808 kJ/mol nm**2,Kangle= 317.5656 kJ/mol rad**2) I half the value of Kb and get the proper dielectric constant (~80) for water reported in paper. If I half Kangle then I dont get proper value. Below are the results for the dielectric constant of water. Bond length is nm. Here I have done some analysis. The original value reported in J. Chem. Phys. 124, 024503 2006, paper are Kbond = 443153.3808 kJ/mol nm**2 Kangle = 317.5656 kJ/mol rad**2. bond lengthKbond angleKangledielectric constant 0.1012 443153.3808113.24 317.5656 ~1.9 : orginal value 0.1012 221576.6904113.24 317.5656 ~80 : 1/2 (Kbond) 0.1012 443153.3808113.24 158.7828 ~1.58 : 1/2 (kangle) 0.1012 221576.6904113.24 317.5656 ~1.9 : 1/2 (Kbond)(Kangle) Here I pasted spc_fw.itp file used for the simulation. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OW 8 15.99940-0.820 A3.1655e-01 6.503e-01 opls_1002 HW 1 1.00800 0.410 A0.00e+00 0.00e+00 [ bondtypes ] ; ij func b0 kb OWHW 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HW OW HW 1 113.24 317.5656 ; J. Chem. Phys. (2006),124,024503 [ moleculetype ] ; Namenrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_1001 1WAT OW 1 -0.82 15.99940 ; 2 opls_1002 1WATHW1 1 0.41 1.008 ; 3 opls_1002 1WATHW2 1 0.41 1.008 ; [ bonds ] ; i
Re: [gmx-users] Re: [gmx-developers] flexible water model
I have general question. If this parameters are not giving the proper results then How come I get the proper results with same parameter if I use 1/2 value of Kbond with the same parameters. I checked the temp when I use half value of Kbond and it goes max. ~320. Nilesh On Wed, May 11, 2011 4:03 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello Justin, I used 0.5 fs time step and still I got dielectric constant ~2. This is the md.mdp file I used. I checked the temperature it didn't go more than ~ 320 K. Still, that's unacceptable if your ref_t is 295. The fact that the temperature is still rocketing up suggests the same instability I found. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 650 ; total 5 ps. nstcomm = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1 nstlist = 1 ns_type = grid rlist = 0.6 rcoulomb= 0.6 rvdw = 0.7 These cutoffs make no sense. The paper you've cited used 0.9 nm. If you're trying to reproduce previous work, use the same settings. coulombtype = PME vdwtype = cut-off Similarly here, you haven't applied dispersion correction, which you should, per the methods used in the JCP article. -Justin pbc = xyz 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 = v-rescale tau_t = 0.1 tc-grps =system ref_t = 295 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 295.0 gen_seed = 173529 Nilesh On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote: The gmx-developers list is not the forum for these types of questions. I am replying via gmx-users, which is where the discussion should stay. I took a few minutes to dig into this. My conclusion is that your system is not stable. I would encourage you to analyze the temperature and pressure of your systems that are giving odd results. When I used the topology you provided, the temperature spiked to over 600 K and the box began to oscillate extensively as if the system were about to explode. The resulting epsilon value was about 1.6. If I reduce the timestep to 0.5 fs, the results are much more reasonable, and using the Ka and Kb values in the paper (not halved!) I get a much more sensible result, even after just 100 ps. It looks to me as if the combination of these parameters and a 1-fs timestep is not entirely stable. I know the original authors used dt = 1 fs, but the point remains. -Justin Nilesh Dhumal wrote: Hello, I am using flexible water model for my system. I am referring a paper J. Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. Kbond = 443153.3808 kJ/mol nm**2 Kangle= 317.5656 kJ/mol rad**2. I am using olss-aa force field parameters in Gromacs VERSION 4.0.7. I checked some papers in which author have used oplsaa force field in Gromacs. 1/2 factor is not in opls force field if I compare opls and amber. I didnt get the proper dielectric constant for water when I used the parameters reported in paper (Kbond = 443153.3808 kJ/mol nm**2,Kangle= 317.5656 kJ/mol rad**2) I half the value of Kb and get the proper dielectric constant (~80) for water reported in paper. If I half Kangle then I dont get proper value. Below are the results for the dielectric constant of water. Bond length is nm. Here I have done some analysis. The original value reported in J. Chem. Phys. 124, 024503 2006, paper are Kbond = 443153.3808 kJ/mol nm**2 Kangle = 317.5656 kJ/mol rad**2. bond lengthKbond angleKangledielectric constant 0.1012 443153.3808113.24 317.5656 ~1.9 : orginal value 0.1012 221576.6904113.24 317.5656 ~80 : 1/2 (Kbond) 0.1012 443153.3808113.24 158.7828 ~1.58 : 1/2 (kangle) 0.1012 221576.6904113.24 317.5656 ~1.9 : 1/2 (Kbond)(Kangle) Here I pasted spc_fw.itp file used for the simulation. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OW 8 15.99940-0.820 A
Re: [gmx-users] Re: [gmx-developers] flexible water model
Nilesh Dhumal wrote: I have general question. If this parameters are not giving the proper results then How come I get the proper results with same parameter if I use 1/2 value of Kbond with the same parameters. Random chance, I imagine. Your .mdp settings are not correct and the cutoffs are unreasonably short for any modern force field. If you're seeking to reproduce others' work, then you have to use the same protocol. You're not doing that. I checked the temp when I use half value of Kbond and it goes max. ~320. This would also indicate instability. You managed to get a correct result for one observable from an incorrect simulation wherein the thermodynamic observables do not correspond to what you have set. The way I found all of this out was first and foremost by watching the trajectory. After about 30 ps, the water molecules freeze in place and vibrate as if they are about to shear apart. At this exact time, the value of epsilon (from epsilon.xvg, output by g_dipoles) plummets down, after having steadily increased for the first 30 ps, as expected. The temperature spikes and the pressure begins to oscillate by +/- 10^5, far higher than what it should for a system of a few hundred water molecules. Watch your trajectories, make sure you're getting the right average temperature and pressure, and that all your other energetic terms stabilize, then analyze the result of the simulation. Otherwise, any inferred output is meaningless. -Justin Nilesh On Wed, May 11, 2011 4:03 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello Justin, I used 0.5 fs time step and still I got dielectric constant ~2. This is the md.mdp file I used. I checked the temperature it didn't go more than ~ 320 K. Still, that's unacceptable if your ref_t is 295. The fact that the temperature is still rocketing up suggests the same instability I found. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 650 ; total 5 ps. nstcomm = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1 nstlist = 1 ns_type = grid rlist = 0.6 rcoulomb= 0.6 rvdw = 0.7 These cutoffs make no sense. The paper you've cited used 0.9 nm. If you're trying to reproduce previous work, use the same settings. coulombtype = PME vdwtype = cut-off Similarly here, you haven't applied dispersion correction, which you should, per the methods used in the JCP article. -Justin pbc = xyz 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 = v-rescale tau_t = 0.1 tc-grps =system ref_t = 295 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 295.0 gen_seed = 173529 Nilesh On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote: The gmx-developers list is not the forum for these types of questions. I am replying via gmx-users, which is where the discussion should stay. I took a few minutes to dig into this. My conclusion is that your system is not stable. I would encourage you to analyze the temperature and pressure of your systems that are giving odd results. When I used the topology you provided, the temperature spiked to over 600 K and the box began to oscillate extensively as if the system were about to explode. The resulting epsilon value was about 1.6. If I reduce the timestep to 0.5 fs, the results are much more reasonable, and using the Ka and Kb values in the paper (not halved!) I get a much more sensible result, even after just 100 ps. It looks to me as if the combination of these parameters and a 1-fs timestep is not entirely stable. I know the original authors used dt = 1 fs, but the point remains. -Justin Nilesh Dhumal wrote: Hello, I am using flexible water model for my system. I am referring a paper J. Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. Kbond = 443153.3808 kJ/mol nm**2 Kangle= 317.5656 kJ/mol rad**2. I am using olss-aa force field parameters in Gromacs VERSION 4.0.7. I checked some papers in which author have used oplsaa force field in Gromacs. 1/2 factor is not in opls force field if I compare opls and amber. I didn’t get the proper dielectric constant for water when I used the parameters reported in paper (Kbond = 443153.3808 kJ/mol nm**2,Kangle= 317.5656 kJ/mol rad**2) I half the value of Kb and get the proper dielectric constant (~80) for water reported in paper. If I half Kangle then I
[gmx-users] index file
Dear users, I have two ligands. I created a special index group that merges the protein, LiGA and LİGB. I have the pr.mdp file as the following: ... energygrps = ProteinLİGA_LİGB tc-grps = Protein_LİGA_LİGBWater_and_ions ... grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr Fatal error: Group LİGA_LİGB not found in indexfile. I get the fatal error since I dont have a special index group that merges LiGA and LİGB. should I create two different index file? Thanks in advance -- Ahmet YILDIRIM -- 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] REMD: after replica exchange breakdown
On 11/05/2011 10:59 PM, SebastianWaltz wrote: On 05/11/2011 05:20 AM, Mark Abraham wrote: On 05/11/2011 02:32 AM, SebastianWaltz wrote: Dear GROMACS User, I'm running a REMD MD of 32 replicas. It worked for the first few replica exchanges. After 30ps again two replicas were exchanged and I received the Error: x particles communicated to PME node y are more than a cell length out of the domain decomposition cell of their charge group The only rationale I can see is that a velocity was scaled after exchange that was now large enough to lead to the normal sort of exploding system. Was the exploding replica going up in temperature? How did you equilibrate the systems? I did a NPT equilibration for each replica which leads obviously to different volumes and looks like to cause some problems. If I use the same volume for each replica it works fine. Yeah, that'd be it. Do the NPT equilibration at your target temperature, and then construct the other replicas to have that volume, before equilibrating each replica at its temperature under NVT. I am using NVT assembles for each replica with a exchanging interval of 5ps. For each replica I use 4 processors. Constraint are only the bonds to hydrogens (constraints = hbonds). Using PME for electro static. Information like GROMACS version, simulation system dimensions and contents would be useful. What replica temperature distribution exists? I am using version 4.0.7. My system consists of a small peptide soluted in ~1500 rigid CHCl3 molecules. System equilibrated with NPT and NVT production run seems to work only if I increase the number of replicas (32-64) meaning that I also decrease the difference of the volumes. The temperature is exponentially distributed from 200 to 450K. Seems OK. Mark When running each replica for its own everything is working fine, nothing is blowing up like one would expect after getting the above Error. Good trouble-shooting :) You'd have been told to try this otherwise... Mark 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] index file
On 12/05/2011 8:23 AM, ahmet yıldırım wrote: Dear users, I have two ligands. I created a special index group that merges the protein, LiGA and LİGB. I have the pr.mdp file as the following: ... energygrps = ProteinLİGA_LİGB tc-grps = Protein_LİGA_LİGBWater_and_ions ... grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr Fatal error: Group LİGA_LİGB not found in indexfile. I get the fatal error since I dont have a special index group that merges LiGA and LİGB. should I create two different index file? You need to give grompp an index file that defines all the groups you use. Yours didn't define LIGA_LIGB, so you need to do so, or to change your energygrps Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] exclusions
On 12/05/2011 2:43 AM, Gavin Melaugh wrote:
Regarding my earlier post- If someone could confirm.
Taking into account that atom indices start from zero.
Then excls[0] = exclusions centred around atom 1.
[0..12] = there are 13 exclusions each one labelled form 0-12.
I then assume that you read the exclusions with respect to atom 0
(actual index =1)
I doubt it. I think each particle excludes itself in the list. Make a
simple system where you can compute the exclusions by hand and see what
the data structure is doing. Then vary it until you're happy with your
deductions.
Mark
In the next set do you read the exclusion with respect to atom 1 (actual
index =2).
and so on
Many thanks in advance
Gavin
Gavin Melaugh wrote:
Hi all
I am cheking the non binary version topol.tpr form grompp and I was
wondering what the following format for the exclusion section signifies?
excls:
nr=228
nra=1920
excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16}
excls[1][13..25]={0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 15}
Also I take it, that this is a result of nrexcl =3
Cheers
Gavin
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[gmx-users] (no subject)
http://howtofindoutifsomeoneismarried.net/wp-content/themes/twentyten/site.html -- 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] about g_hbond
/* y-label: Hydrogen Bond Index */
is it relevant to the total number of hydrogen bonds?
such as
/* XPM */
/* x-label: Time (ps) */
/* y-label: Hydrogen Bond Index */
/* type:Discrete */
static char *gromacs_xpm[] = {
A-b : 51 84 2 1,
b-C : 51 95 2 1,
84, 95?
Thanks,
On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
Hi,
For group A, b, C.
It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
But I don't know how to get the number of residues of b forming both
with A and B at the same time. namely b-AC, not with AC group.
There's no direct way to do it, but from the output files of g_hbond it can
be done. You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
some script that parses the .xpm files, and whenever there is an entry of
A-C in the same frame as B-C, then you have a hydrogen bond mediated between
the two.
There's lots of discussion in the list archive about water-mediated
hydrogen bonds that is likely applicable here.
Note that if you're using g_hbond in version 4.5, there is an important bug
that was fixed just yesterday:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
-Justin
Thanks,
--
Best Regards,
lina
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Best Regards,
lina
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