[gmx-users] g_analyze
Dear all
When I use the following command:
g_analyze -ffree_bi_0.9.xvg -av average_0.9
I got
set average standard deviation *std. dev. /
sqrt(n-1)*…
SS16.053822e+01 3.062230e+01 1.936724e-02…
What is “*std. dev. / sqrt(n-1)” *?
I know that
Standard deviation (SD) for samples is quall to sqrt[{sum((x-xmean)*2)/n-1}]
Standard error* *(SE) = Standard deviation/sqrt( n)
n is number of samples.
But I don’t know what is the concept of the “*std. dev. / sqrt(n-1)”*? is
it SE?
Sincerely
Afsaneh
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[gmx-users] Standard errors
Dear all I would like to calculate the standard deviation (as the error bar) for dV/dlanda.xvg file. I used g_analyze command as the following: g_analyze -ffree_bi_0.9.xvg -av average_0.9 I got: set average *standard deviation* *std. dev. / sqrt(n-1)*… SS16.053822e+01 3.062230e+01 1.936724e-02… Is the amount of in third (standard deviation) or fourth column (std. dev. / sqrt(n-1) ) better than to use as the standard errors? I want to draw dG/d lambda via lambda and show error bar for free energy. Thanks in advance Afsaneh -- 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] Error bar for free energy
Hi Dear Gromacs users, I would like to calculate the standard deviation (as the error bar) for dV/dlambda.xvg file. I used g_analyze command as the following: g_analyze -ffree0.9.xvg -av average_0.9 I got: set average*standard deviation**std. dev. / sqrt(n-1)*… SS1 6.053822e+01 3.062230e+01 1.936724e-02 … Is the amount of in third (standard deviation) or fourth column (std. dev. / sqrt(n-1) ) better than to use as the error bar? I want to draw dG/d lambda via lambda and show error bar for free energy differences. Thanks in advance Afsaneh -- 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] Invalid order for directive atomtypes
Dear GMX users, To generate a topology file for an arbitrary molecule (TP) on graphite surface, I used g_x2top program to generate “TP.itp” file and I manually construct graphite.itp file. Generated topology file is as the following: #include ./oplsaa.ff/forcefield.itp #include TP.itp #include graphite.itp [ system ] TP ON GRAPHITE [ molecules ] ;molecule namenr. TP2 grap6400 ……. And the graphite.itp is as the following: [ moleculetype ] ; name nrexcl grap 1 [ atoms ] ; nr typeresnrresidu atomcgnr charge 1 opls_145 1 grap C 1 0.000 I run grompp for EM with this command line: grompp -f *.mdp –c *.gro -p *.top -o *.tpr It gave me the following error: ……… Fatal error: Syntax error - File ffnonbonded.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ……. I know things in the [ molecules ] section need to line up with what's in the *.gro file. Also I looked at that link but I don’t know how to solve this problem. And other question is: Do I need to make “nonbonding.itp” to insert in topology file for introducing nonbonding interaction of graphite with TP molecule? Sincerely Afsaneh -- 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] atomtypes in .n2t
Dear users To generate a topology file for an arbitrary molecule, I used g_x2top program. I added following lines to atomname2type.n2t: .. .. C opls_145B 0.080627 12.0110 3 C 0.1395 C 0.1395 C 0.149 C opls_145B 0.091698 12.0110 3 C 0.149 C 0.1395 C 0.1395 .. But, generated topology file is as the following: . [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB .. .. 17 opls_145 1TPTC15 1 0.037549 12.011 ; qtot -0.4087 18 opls_145 1TPTC12 1 0.037549 12.011 ; qtot -0.3712 .. I don’t know, why g_x2top program replaces opls_145B (in .n2t) with opls_145 atom type to generate topology file? Thanks in advance, Afsaneh -- 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] .n2t file format
Dear gmx users I scrap lines from some files in oplsaa.ff folder as the following ffnonbonded file: [ atomtypes ] opls_157 CT6 12.01100 0.145 A3.5e-01 2.76144e-01 atomtypes.atp file: opls_157 12.01100 ; all-atom C: CH3 CH2, alcohols also, I looked at /gromacs /Documentation/file format/.n2t that written: To translate atom names into atom types, the x2top program uses library files called .n2t files as input. These files contain information about atom types, charges, and connectivity to neighbors. The format of such a file is exemplified by: *C* opls_157 -0.18 12.011 4 H 0.108 H 0.108 H 0.108 C 0.150 The above line interprets an atom named C to be the carbon atom in CH3, CH2, or alcohols (atom type opls_157). My question is that carbon atomname with opls_157 atomtype is *C* or CT? In other word the first column in .n2t is atomneme (CT as mentioned in ffnonbonded file ) or element name (C as mentioned in file format.n2t )? Also, are 6, 8 10 columns atomname or element name? Any help is much appreciated Afsaneh -- 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] Generate topology
Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Thanks in advance, Afsaneh -- 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] Generate topology
Dear Justin thanks for your reply, I did it. when I put the .n2t in my working directory,I have gotten this error. thanks in advance, Afsaneh -- 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] Generate topology -2
Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I edited atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms for more information and tips for troubleshooting, ……….. I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as the above mentioned in my working directory. How to solve my problem? Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? Thanks in advance, Afsaneh -- 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] Generate topology
Dear Justin I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as mentioned in before post in my working directory. I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ……….. I seem can't read atomname2type.n2t file from my working directory. Thanks very much. Afsaneh On Fri, Jul 19, 2013 at 5:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/19/13 8:53 AM, afsaneh maleki wrote: Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Put the .n2t file in the working directory, not in an oplsaa.ff subdirectory. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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
[gmx-users] Adjust time intervals
Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- 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] Adjust time intervals
Thanks Dear Peter and Justin for reply, I paste some text from .mdp for calculation of free energy. I have done calculation of minimization energy before. title = production for ile-pro-SOL ; Run parameters integrator= sd ; leap-frog integrator nsteps= 100 ; 0.002* 100 = 2000 ps (2 ns) dt = 0.002 ; 2 fs tinit =0 ; Output control nstxout = 10; save coordinates every 0.2 ps nstvout =10 ; save velocities every 0.2 ps nstxtcout =10 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps xtc_precision =1000 ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints= all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS unconstrained_start=no lincs_order=12 lincs_warnangle=30 shake-tol =0.0001 ; Neighborsearching ns_type = grid; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1.2 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 1. rvdw =1.1 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on ;tcoupl = Nose-Hoover ; More accurate thermostat ;pcoupl =Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic tau_p= 5.0 ; time constant, in ps ref_p= 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 ;restraints ;dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme Thanks, Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: Peter C. Lai wrote: In the .mdp file what is nstenergy set to? I'd further ask what the rest of the .mdp file says, as well. If this is the output of energy minimization, it's totally normal. The output seems irregular but is due (I believe) to the potentially uneven step size taken during EM. -Justin On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- 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. 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
Re: [gmx-users] Adjust time intervals
Dear Justin, I use version 4.0.7 Thanks Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Thanks Dear Peter and Justin for reply, I paste some text from .mdp for calculation of free energy. I have done calculation of minimization energy before. Which Gromacs version are you using? I can't reproduce your problem with version 4.5.4 or 4.5.5, either with or without the free energy code. My energy outputs are always present at the nstenergy interval. -Justin title= production for ile-pro-SOL ; Run parameters integrator = sd ; leap-frog integrator nsteps = 100 ; 0.002* 100 = 2000 ps (2 ns) dt = 0.002 ; 2 fs tinit =0 ; Output control nstxout = 10; save coordinates every 0.2 ps nstvout =10 ; save velocities every 0.2 ps nstxtcout =10 ; xtc compressed trajectory output every 2 ps nstenergy= 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps xtc_precision =1000 ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS unconstrained_start=no lincs_order=12 lincs_warnangle=30 shake-tol =0.0001 ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1.2 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 1. rvdw =1.1 ; Electrostatics coulombtype= PME ; Particle Mesh Ewald for long-range electrostatics ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on ;tcoupl= Nose-Hoover ; More accurate thermostat ;pcoupl=Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype= isotropic tau_p = 5.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5; isothermal compressibility, bar^-1 ;restraints ;dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ; Periodic boundary conditions pbc= xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme Thanks, Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: Peter C. Lai wrote: In the .mdp file what is nstenergy set to? I'd further ask what the rest of the .mdp file says, as well. If this is the output of energy minimization, it's totally normal. The output seems irregular but is due (I believe) to the potentially uneven step size taken during EM. -Justin On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- 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
Re: [gmx-users] g_sas
Hi, Thanks dear Justin for useful reply, I have a system that is contained of protein-water-ions. I want to calculate residue SAS of protein. In the first way, I select a group consisting protein for calculation, and then this protein for output. At the second way, I select the whole system first for calculation, and then protein for output. The SAS_calculations of residue protein are different in two ways. I have two questions. Q1- Why results are different in two ways? Q2-Can anyone demonstrates clearly how residue SAS of protein calculate in two ways? Q3- what property or quantity do I can get from The SAS_calculations of residue protein in two ways? Best wishes, Afsaneh On 3/15/12, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc I select the whole protein first for calculation, and then this protein for output.In this way I can obtain Area per residue from res_area file and area per atom from atom_area file. How to get area per residue with data of area per atom from atom_area file? When I average on area per atoms for a selected residue, it doesn't correspond with area per residue for a selected residue from res_area. It shouldn't. Averaging the areas per atom should not produce anything related to the constituent residue(s). The sum of the atom areas should yield the residue area. A quick look through the code seems to indicate that this is true, that is, the two quantities are not produced independently; residue area arises from atom area. -Justin How to correlate area per residue for a selected residue with area per atoms for a selected residue? Thanks in advance, Afsaneh -- 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 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_sas; could not find a Van der Waals radius
Hi, I have a system that is contained of Protein-DOPC-SOL-Ions. I want to calculate residue SAS of protein.The calculation group consists of all the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14 ion),and then protein for output. Force files used for protein and DOPC are ffg53a6 and Berger respectively. When I use g_sas I obtain the following message: WARNING: could not find a Van der Waals radius for 125 atoms. I have two questions. Q1- This warning is important? Q2-Is the valid source to get data for Van der Waals radius of phosphorous atom to insert in the vdwradii.dat file? I think this warning is about phosphorous atoms of DOPC. what is Van der Waals radius of phosphorous atoms that will be right for this goal? Thanks very much in advance, afsaneh -- 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_sas
Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc I select the whole protein first for calculation, and then this protein for output.In this way I can obtain Area per residue from res_area file and area per atom from atom_area file. How to get area per residue with data of area per atom from atom_area file? When I average on area per atoms for a selected residue, it doesn't correspond with area per residue for a selected residue from res_area. How to correlate area per residue for a selected residue with area per atoms for a selected residue? Thanks in advance, Afsaneh -- 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_sas
Dear user, I have a system that is contained of protein-water-ions. There, I select the whole protein first for calculation, and then this protein for output. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc In this way I can obtain Area per residue from res_area file and area per atom from atom_area file. How to get area per residue by data of area per atom from atom_area file? When I average on area per atoms for a selected residue, it doesn't correspond with area per residue for a selected residue from res_area. How to correlate area per residue for a selected residue with area per atoms for a selected residue? Thanks in advance, Afsaneh -- 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_dist without output file
On 3/10/12, lina lina.lastn...@gmail.com wrote: On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Lina There is not any things related to list of atoms on the terminal. Might your distance -dist so large. try a smaller one and see. Best regards -- 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 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 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] Warning: g_sas Vdwradii.dat
Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Justin. I had not added van der Waals of phosphor for phosphor in vdwradii.dat, when I did simulation. It seem that it use the default value of 0.12 nm. When I use g_sas command, I get the following warning: WARNING: could not find a Van der Waals radius for 125 atoms I have two questions. Q1) Do I add radius of van der Waals of phosphor in vdwradii.dat ? Or Ignore this warning in this time. I couldn't find the reference that report radius of van der Waals for elements like what is in vwdradii.dat. For example see this address http://www.webelements.com Q2) would you please get me exact reference to find radius of van der Waals of phosphor that match with other elements in vdwradii.dat? 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
[gmx-users] g_sas vdwradii.dat
Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Dr. Justin. I had not added van der Waals radius of phosphorous in the vdwradii.dat file, when I did simulation. It seem that it use the default value of 0.12 nm. When I use g_sas command, I get the following warning: WARNING: could not find a Van der Waals radius for 125 atoms I have two questions. Q1) Can I add radius of van der Waals of phosphorous in vdwradii.dat after simulation? or should i repeat simulation again? I couldn't find the reference that report radius of van der Waals for elements like what is in vwdradii.dat. For example see this address http://www.webelements.com Q2) would you please get me exact reference to find radius of van der Waals of phosphor that match with other elements in vdwradii.dat? 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] Coulomb Energies
On 12/17/11, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote: Dear Gromacs experts, I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14 show high RMSD then what should we interpret from such results?? Average Coulomb Energy (kJ/mol) -1.62657e+06 RMSD 2236.85 Error Estimation 150 Total drift (kJ/mol) -894.82 Many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] do_dssp
Hi, I'm trying to use do_dssp of gromacs 4.5.4 in fedora core . I did processes of Download , Uncompress and Compile the source code as the following unzip dsspcmbi.zip cd dssp [root@localhost dssp]# ./DsspCompileGCC That i got this message: Running script to compile the CMBI version of DSSP, please wait... /usr/bin/ld: cannot find -lm collect2: ld returned 1 exit status Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program... I googled but i don't find clear way to solve this problem. can help me? Afsaneh -- 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 install FFTW 3.2.2
Hi, To compile a single-precision version of the libraries and install FFTW version 3.2. I followed the steps inhttp:// www.gromacs.org/Downloads/Installation_Instructions#Prerequisites . my computer characteristics: Root at …fftw-3.2.2]# uname -a Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 21:25:57 EST 2009 i686 i686 i386 GNU/Linux I used the following command: Root at …fftw-3.2.2]# ./configure --enable-threads --enable-float --enable-sse Root at …fftw-3.2.2]make I get these errors: make[3]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools' make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools' Making all in m4 make[2]: Entering directory `/home/afsaneh/m/fftw-3.2.2/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/m4' make[1]: Leaving directory `/home/afsaneh/m/fftw-3.2.2' I used make distclean and try to configure again with. Root at …fftw-3.2.2]#./configure --enable-threads --enable-float --enable-sse --disable-shared Root at …fftw-3.2.2]#./configure --enable-threads --enable-float --enable-sse --enable-shared Root at …fftw-3.2.2]#./configure --enable-threads --enable-float --enable-sse --with-pic Root at …fftw-3.2.2]#./configure --enable-threads --enable-float --enable-shared Root at …fftw-3.2.2]#./configure --enable-threads --enable-float --with-pic I get the same errors during FFTW version 3.2.2 compilation (the make step) as above. What commands are useful for compiling FFTW version 3.2.2 on my computer? Thanks in advance, Afsaneh -- 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 install gromacs 4.5.1
Hi, My characteristics computer: Root at …fftw-3.2.2]# uname -a Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 21:25:57 EST 2009 i686 i686 i386 GNU/Linux To install FFTW version 3.2.2. I used the following commands: Root at …fftw-3.2.2]# ./configure --enable-threads --enable-float --enable-shared Root at …fftw-3.2.2]# make Root at …fftw-3.2.2]# make install After using “make” and “make install”, it get me the following text at end: make[3]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools' make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools' Making all in m4 make[2]: Entering directory `/home/afsaneh/m/fftw-3.2.2/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/m4' make[1]: Leaving directory `/home/afsaneh/m/fftw-3.2.2' .. To install gromacs version 4.5.1 root@localhost gromacs-4.5.1]#./configure * On most platforms you can save 10X space with dynamic libraries, although the binaries might be less portable. Why not try --enable-shared ? [root@localhost gromacs-4.5.1]#make [root@localhost gromacs-4.5.1]#make install [root@localhost gromacs-4.5.1]# make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done when i used each command with” –h” or “–help” I obtain the followinf error: [afsaneh@localhost ~]$ g_analyze -h g_analyze: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such file or directory [afsaneh@localhost ~]$ editconf -h editconf: error while loading shared libraries: libfftw3f.so.3: cannot open shared object file: No such file or directory How to solve this problem? Best wishes, Afsaneh -- 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] Contribution of delta bonding energy in the delta free energy
Hi, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane. I want to separate contributions of delta bonding and nonbonding energy in delta Gibbs energy. Best wishes, Maleki, -- 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] Contribution of delta bonding energy in the delta free energy
Dear Mark, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane with dual topology. topology A (lambda=0) to topology B (lambda=1) What i obtained after using mdrun command to calculate free energy is dgdl.xvg that contain dV(total)/dlamda via time. I want to obtein dV(bond)/dlamda and dV(non-bond)/dlamda, seperetly. dV(bond)/dlambda and dV(non-bond)/dlambda are not writed in free.edr and free.log. how to produce dv(bond)/dlambda and dV(non-bond)/dlambda. my version gromacs is 4.0.5 and 4.0.7. Thanks in advance, Maleki On Tue, Aug 9, 2011 at 6:18 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/08/2011 9:13 PM, afsaneh maleki wrote: Hi, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane. I want to separate contributions of delta bonding and nonbonding energy in delta Gibbs energy. So instead of using the sum of bonded and non-bonded energy (i.e. total PE), use them separately. Whether that will mean anything is up to you to demonstrate. Mark Best wishes, Maleki, -- 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] Vectors in non-cubic box
Hi, I want to create *.gro file with simulation box size as following: 3.460467452 0. 0. 1.730233726 2.9968527222000 0. 0. 0. 10.00 I used the command: ]editconf –f *.pdb –o *.gro –box 3.46 3.46 10.–c–angle 90 90 60 are these commands proper to create this simulation box size? system size : 4.975 2.951 0.084 (nm) center : 0.025 0.548 0.966 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 2.570 0.951 4.034 (nm) new center : 2.595 1.498 5.000 (nm) new box vectors : 3.460 3.460 10.000 (nm) new box angles : 90.00 90.00 60.00 (degrees) new box volume : 103.68 (nm^3) Also I paste some .gro file 1 NAU 39 1.759 1.647 4.998 1 HAC 41 1.855 1.618 4.993 1 HAB 40 1.686 1.578 5.002 3.46000 2.99645 10.0 0.0 0.0 1.73000 0. -0. -0.0 What is three last values in box vector,0.00 -0.00 -.0 0? Would one please clear me about these vectors? 3.46000 2.99645 10.0 0.0 0.0 1.73000 0. -0. -0.0 xx yy zz ? ? xy ?? ? I have another question that does g_hbond has the compatibility with non-cubic (or parallelpiped) cells? good luck Afsaneh -- 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] Vectors in non-cubic box
Thanks Dear Tsjerk g_hbond has the compatibility with non-cubic (or parallelpiped) cells? Best wishes, Afsaneh -- 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] pressure coupling not enough values (I need 2)
Hi, grompp show the error as below: ERROR: pressure coupling not enough values (I need 2) I used ref_p =1. In file.mdp How to solve this problem? thanks in advance, Afsaneh -- 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] dgdl.xvg file
Hi, Is there command in .mdp to adjust of frequency to write dg/dlamda to dGdL.xvg file? I do mdrun for 100 steps, so I get 100 dg/dl in dgdl.xvg file while I want to change output to write 1000 dgdl in dGdL.xvg file. How can I do? thaks in advance, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Overriding atomtype O
Hi, I have a problem with grompp. I want to simulate membrane protein. I adjust the [ molecules ] section to list the number and type of my components I run grompp and it shows 56 warning about all of atom types in ffG53a6nb.itp (56 atom types are in ffG53a6). I run pdb2gmx for protein only. Why does it give me these warning? I paste warning here: Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp WARNING 1 [file ffG53a6nb.itp, line 3]: Overriding atomtype O WARNING 2 [file ffG53a6nb.itp, line 4]: Overriding atomtype OM WARNING 3 [file ffG53a6nb.itp, line 5]: Overriding atomtype OA WARNING 4 [file ffG53a6nb.itp, line 6]: Overriding atomtype OE WARNING 5 [file ffG53a6nb.itp, line 7]: Overriding atomtype OW WARNING 6 [file ffG53a6nb.itp, line 8]: Overriding atomtype N WARNING 7 [file ffG53a6nb.itp, line 9]: Overriding atomtype NT WARNING 8 [file ffG53a6nb.itp, line 10]: Overriding atomtype NL WARNING 9 [file ffG53a6nb.itp, line 11]: Overriding atomtype NR WARNING 10 [file ffG53a6nb.itp, line 12]: Overriding atomtype NZ WARNING 11 [file ffG53a6nb.itp, line 13]: Overriding atomtype NE WARNING 12 [file ffG53a6nb.itp, line 14]: Overriding atomtype C WARNING 13 [file ffG53a6nb.itp, line 15]: Overriding atomtype CH0 WARNING 14 [file ffG53a6nb.itp, line 16]: Overriding atomtype CH1 WARNING 15 [file ffG53a6nb.itp, line 17]: Overriding atomtype CH2 WARNING 16 [file ffG53a6nb.itp, line 18]: Overriding atomtype CH3 WARNING 17 [file ffG53a6nb.itp, line 19]: Overriding atomtype CH4 WARNING 18 [file ffG53a6nb.itp, line 20]: Overriding atomtype CH2r WARNING 19 [file ffG53a6nb.itp, line 21]: Overriding atomtype CR1 WARNING 20 [file ffG53a6nb.itp, line 22]: Overriding atomtype HC WARNING 21 [file ffG53a6nb.itp, line 23]: Overriding atomtype H WARNING 22 [file ffG53a6nb.itp, line 24]: Overriding atomtype DUM WARNING 23 [file ffG53a6nb.itp, line 25]: Overriding atomtype S WARNING 24 [file ffG53a6nb.itp, line 26]: Overriding atomtype CU1+ WARNING 25 [file ffG53a6nb.itp, line 27]: Overriding atomtype CU2+ WARNING 26 [file ffG53a6nb.itp, line 28]: Overriding atomtype FE WARNING 27 [file ffG53a6nb.itp, line 29]: Overriding atomtype ZN2+ WARNING 28 [file ffG53a6nb.itp, line 30]: Overriding atomtype MG2+ WARNING 29 [file ffG53a6nb.itp, line 31]: Overriding atomtype CA2+ WARNING 30 [file ffG53a6nb.itp, line 32]: Overriding atomtype P WARNING 31 [file ffG53a6nb.itp, line 33]: Overriding atomtype AR WARNING 32 [file ffG53a6nb.itp, line 34]: Overriding atomtype F WARNING 33 [file ffG53a6nb.itp, line 35]: Overriding atomtype CL WARNING 34 [file ffG53a6nb.itp, line 36]: Overriding atomtype BR WARNING 35 [file ffG53a6nb.itp, line 37]: Overriding atomtype CMet WARNING 36 [file ffG53a6nb.itp, line 38]: Overriding atomtype OMet WARNING 37 [file ffG53a6nb.itp, line 39]: Overriding atomtype NA+ WARNING 38 [file ffG53a6nb.itp, line 40]: Overriding atomtype CL- WARNING 39 [file ffG53a6nb.itp, line 41]: Overriding atomtype CChl WARNING 40 [file ffG53a6nb.itp, line 42]: Overriding atomtype CLChl WARNING 41 [file ffG53a6nb.itp, line 43]: Overriding atomtype HChl WARNING 42 [file ffG53a6nb.itp, line 44]: Overriding atomtype SDmso WARNING 43 [file ffG53a6nb.itp, line 45]: Overriding atomtype CDmso WARNING 44 [file ffG53a6nb.itp, line 46]: Overriding atomtype ODmso WARNING 45 [file ffG53a6nb.itp, line 47]: Overriding atomtype CCl4 WARNING 46 [file ffG53a6nb.itp, line 48]: Overriding atomtype CLCl4 WARNING 47 [file ffG53a6nb.itp, line 49]: Overriding atomtype FTFE WARNING 48 [file ffG53a6nb.itp, line 50]: Overriding atomtype CTFE WARNING 49 [file ffG53a6nb.itp, line 51]: Overriding atomtype CHTFE WARNING 50 [file ffG53a6nb.itp, line 52]: Overriding atomtype OTFE WARNING 51 [file ffG53a6nb.itp, line 53]: Overriding atomtype CUrea WARNING 52 [file ffG53a6nb.itp, line 54]: Overriding atomtype OUrea WARNING 53 [file ffG53a6nb.itp, line 55]: Overriding atomtype NUrea WARNING 54 [file ffG53a6nb.itp, line 56]: Overriding atomtype SI WARNING 55 [file ffG53a6nb.itp, line 57]: Overriding atomtype MNH3 WARNING 56 [file ffG53a6nb.itp, line 58]: Overriding atomtype MW Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 825 of the 2346 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Opening library
[gmx-users] dgdl.xvg
Hi, Is there command in .mdp to adjust of frequency to write dg/dlamda to dgdl.xvg file? I do mdrun for 100 steps, so I get 100 dg/dl in dgdl.xvg file while I want to change output to write 1000 dgdl in dGdL.xvg file. How can I do? Thanks in advance. thanks very much, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] moleculetype CU1+ is redefined
Hi, When I generate the tpr file with grompp, I get the following error. Fatal error: moleculetype CU1+ is redefined I work on membrane protein that have no atomtype CU1+. why i get error on CU+? I have cheked [moleculetypes] in toplogy file and there are n't doplicated. How to remove this error? thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] ions.itp
Dear justin, thanks for your helpful reply. where Gromacs does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. why in ions.itp #ifdef _FF_GROMACS is defended? Best wishes, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: moleculetype CU1+ is redefined
this error is removed. becuse ion.itpwas included twice in .top and .itp files. i have included two FF into topology file, one for protein and another one for bilayer. Afsaneh On Mon, Jun 14, 2010 at 6:07 PM, Vitaly Chaban vvcha...@gmail.com wrote: When I generate the tpr file with grompp, I get the following error. Fatal error: moleculetype CU1+ is redefined I work on membrane protein that have no atomtype CU1+. why i get error on CU+? I have cheked [moleculetypes] in toplogy file and there are n't doplicated. How to remove this error? How many FF files have you included into the topology file? Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Solvation free energy
Hi, I want to calculate the solvation free energy of Wild-type human IAPP (hIAPP) with 37 residues in length that residu26 isoleucine is mutated to proline (ile26pro). I used dual topology in Thermodynamic integration (TI) for calculating salvation free energy. For the solvation free energy calculations I need some parameter as *Sc_alpha*, *Sc_power* and *Sc_power * in* *mdp file. I also read manual of Dr David van der spoel about salvation free energy and manual of Gromacs. Nevertheless, I couldn’t decide best value for these parameters and my protein. I used the following values in mdp file: free_energy = yes init_lambda = 0.00 sc_alpha= 0.5 sc_power= 1.0 sc_sigma= 0.3 What values do you suggest for these parameters? Thanks very much, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] mutation to/from proline
Hi, I want to calculate relative free energy associated to mutation of P1 (native protein) to p2 (mutated protein).In this mutation, Isolusine (in P1) is mutated to Proline(in P2). With using Thermodynamic cycle: Bilayer+P1= = = Bilayer-P1 delta G1 (association P1) Bilayer+P2= = = Bilayer-P2 delta G2 (association P2) Where P1 = = = P2 deltaG3 Bilayer-P1 = = = Bilayer-P2 deltaG4 So, delta deltaG= (delta G1(association P1)- deltaG2 (association P2))= (deltaG3- deltaG4) To define the B state that will be used for the free energy calculation. For this; I need to specify the new atom type of each mutated atom and the set of parameters to it. But my question is that with regarding to special structure of proline, is it possible to update topology file? Who was done mutation of proline before? I searched but I didn’t find! Or is there manual for mutating from/to proline? I appreciate your help, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Thickness
Hi, I used bilayer that consisted of 128 DOPC lipids as DOPC128.pdb as the primary bilayer and insert protein in bilayer with Inflategro program. when i expanded the bilayer, two DOPC molecules exited from box. i simulated this system and obtained the thickness of bilayer with GrigMAT_MD. i want to subtract the thickness of pure bilayer from the bilayer that contain the protein. would one please elaborate step by step how to subtract the thickness of the pure bilayer( 128 DOPC) from the bilayer (126 DOPC) that contains the protein to get two-dimensional maps of ∆Z that indicate deviation from the thickness of pure bilayer ? Thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] free energy
Hi, I inserted the protein in bilayer at Z normal and simulated membrane protein. to calculate free energy, it is better to use umbrella sampling tutorial from Justin Lemkul or free energy tutorial from David Mobley for my system? thanks, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Energy per residue
Dear gromacs users, Is there a way to get energy values (Vdw,..) per residue at the end of MD prosses? I would really appreciate any help. Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Energy per residue
Dear Justin, I want to get energy per residue not time. if i use mdrun -rerun with energygrps in md.mdp then g_energy i obtain enery per time not residue. at last, i don't understand how to get Energy per residue . Best wishes, Afsaneh afsaneh maleki wrote: Dear gromacs users, Is there a way to get energy values (Vdw,..) per residue at the end of MD prosses? Yes and no. You won't be able to get, for instance, the absolute van der Waals energy of a residue. That doesn't really make any sense, since vdW interactions take place between particles. There may be some 1-4 type interactions within a residue that you could quantify, but not much else. You can decompose short-range residue-residue energies using energygrps in the .mdp file, and re-running the trajectory with the new .tpr file (mdrun -rerun), but the .edr file can quickly get out of hand in terms of disk usage, depending on how many groups you have (since you will then have essentially N^2 energy terms to write out, where N is the number of energygrps). -Justin I would really appreciate any help. Afsaneh -- 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/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/mailing_lists/users.php
[gmx-users] order parameter for UAFF model
Hi all, i used united the atom force field model for the membrane lipids . to calculate order parameter i used : g_order -od -d i know united atom force field doesn't have hydrogen atoms in hydrocarbons chains . i want to know gromacs calculates order parameter * Sc-c* or *Sc-d*(Deuterium) ? in the output is written: title Deuterium order parameters thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Energy via residue
Hi all, How do i obtain the protein van der waals and electrostatic energies with bilayer via residue? highly appreciate!! Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] hblife
Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] hblife
thanks dear justin' it is right that the output of the analysis tools generally writes axis labels and data set legends. in hblife.xyg file is written that x axis label Time (ps) and the last time is written 14300.001 whereas my simulated time is 4 ps not 143000.00 ps i send you this file Best wishes, Afsaneh On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? Check the headers in the .xvg file; the output of the analysis tools generally writes axis labels and data set legends. If it still doesn't make sense, post a snippet of your file. -Justin thanks in advance, Afsaneh -- 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/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/mailing_lists/users.php -- hblife.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] The most probable secondary structure
Hi, how do i obtain the most probable secondary structure for each residue to analyze the detailed conformation of the peptide? i used do_dssp then converted *.eps to *.ps then obtained secondary structure. highly appreciate!! Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Density Profile
Hi, I obtained the electron density profile for the solvent in protein membrane simulation, For this I used the following commands: ]$ g_density -f md.xtc -s md.tpr -d z -dens electron -o sol.xvg -ei electrons.dat -symm -n index.ndx Although in md.gro file is seen any water in middle box (hydrophobic region) simulation, Plot shows the electron density of the water is higher in the middle bilayer than the edges. Would any help me to remove this problem? are commands used correctly? Best regards, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Electron Density
Hi, I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3 OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? Best wishes, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Electron Density2
Dear David van der Spoel, Would you please elaborate on the details? I didn’t underestand about “remove = sign” thanks in advans, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Electron Density3
Hi , I want to obtain electron density for solvent in z direction for bilayer. I used following options: ] g_density -f md.xtc -s md.tpr -d z -dens electron -o electrondens.xvg -ei electrons.dat -symm -n index.ndx Atomtapes in md.gro are OH,HW1,HW2 And “electrons.dat” file contains: 3 OW= 8 HW1=1 HW2=1 But I get error: Fatal error: Invalid line in datafile at line 1 What is my error? Would you please elaborate on the details? thanks in advance very much, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] order parameter for unsaturated chains
Hi, I want to obtain order parameter for unsaturated carbons (eg. 9, 10) on oleoyl (18 carbons) chains. i use -Scd= 2/3 Sxx +1/3 Syy for the saturated carbons. I try to calculate order parameters for unsaturated carbons, which is defined as: Scd=1/4Szz + 3/4 Syy + sdr(3)/2 Syz , with ignore third term (sqr(3)/2 Syz) : but i don't know do i use this correlation for 8, 9 carbons or 9,10 ? because the segmental vector Cn-1 to Cn+1 is taken as the molecular axis of the Cn methylene group. thanks in advans, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] MSD
Hi, I am working on the simulation of protein memberane. How can I calculate MSD (mean squar displacement) of bond lipid ( as those phosphate atomes are written 0.35 nm of protein)? I know that I must use g_msd for calculating, but I need “index file” that is included phosphate atoms within 0.35 nm of protein. how can I obtain this index file thanks in advance, Afsaneh Maleki -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] grompp error in peptide-membrane simulations
Hi, I am working on memberane peptide simulation under lipid DOPC,i have downloaded the lipid and dopc.itp from the same site,when i run grommp: ]grompp -f em.mdp -c complex.gro -o em.tpr -p complex.top it gives me: Fetal error : Atomtype LC3 not found! (this is atomtype of the lipide) This is my complex.top file #include protein.itp #include dopc.itp #include lipid.itp #include tip3p.itp #include ions.itp [system] ;name protein on sur+relaxed dopc [molecules] ;namenumber Protein 1 DOPC 128 SOL 4086 SOD 6 CLA 8 --- this atomtype (LC3) is in the dopc.itp and lipid.itp files but don't find in ffG43a2.rtp and .atp. i'm sure structure file is n't different in terms of the number of atoms , atomnames and the order of them with .itp files. any help will be hightly appreciated. -- Afsaneh Maleki PhD student of physical chemistry Department of chemistry, Isfahan Univ. of Tech. Isfahan 84156-83111, Iran ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
