[gmx-users] what does the "Coulomb (SR) mean under PME?
Hi all, Anybody can help me out! Thanks in advance? In my test simulation, there are one Na^+ and one Cl^- (the distance of 1nm) in vacuum in a very big simulation box (10*10*10 nm^3). I calculated the energies under two different conditions, "coulombtype=PME" vs "coulombtype=cut-off". 1. "coulombtype=PME" Coul. recip. -139.191 -- 0 0 (kJ/mol) Coul-SR:NA-CL*-0.0322805* -- 0 0 (kJ/mol) LJ-SR:NA-CL -0.00100285 -- 0 0 (kJ/mol) 2. "coulombtype=cut-off" Coul-SR:NA-CL * -138.935* -- 0 0 (kJ/mol) LJ-SR:NA-CL -0.00100285 -- 0 0 (kJ/mol) I did some calculations. Under "coulombtype=cut-off", E(Coul-SR) = f*e_i*e_j/r with f=138.935, which is what I expect. However under "coulombtype=PME", how does Gromacs get the value of -0.0322805kJ/mol for "*SR*" term? If I understand it correctly, "SR" means "short-range", which is within the cut-off distance. Since the cut-off distance (1.2nm here) is much smaller than the simulation box length (10nm), there is not short-range interaction with the image box. Some details: Gromacs 4.5.5 PBC is used. distance of Na^+ and Cl^-: 1nm Na^+ and Cl^- are frozen in XYZ dimensions. Only 1 step is run. best regards, Baofu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: implicit wall doesn't recognize the wall_atomtype correctly?
Hi, Firstly, regarding my last email, even though I didn't get any complain about the nonsense setting for the wall_atomtype from grompp, the mdrun is crashed after some steps. Then I tested some atomtypes which have been given in OPLS, and checked the output in md.log: a) When "wall_atomtype = opls_135" in .mdp, *wall_atomtype[0]=2*(wall_atomtype[1]=2) in md.log. b) When "wall_atomtype = SI" in .mdp, * wall_atomtype[0]=9*(wall_atomtype[1]=9) in md.log. c) When "wall_atomtype = opls_1001" in .mdp, *wall_atomtype[0]=9*(wall_atomtype[1]=9) in md.log, where opls_1001 is the atome type for graphene carbon added by myself. Does anyone know about why the md.log give different result from the .mdp file? and what does the *wall_atomtype[0]=2 (or 9)* means? Thanks a lot in advance! best wishes, Baofu Qiao 2010/1/15 Baofu Qiao > Hi all, > > I want to know whether it is a bug or not: When I use some nonsense > wall_atomtype for the implicit wall, the grompp doesn't complain about it. > Or it is a mistake I make myself. > I am using gmx 4.0.7. See the following flags of wall_atomtype. > > nwall= 2 > wall_type= 9-3 > wall_r_linpot = 0.1 > wall_atomtype= *abc 123;opls_abc opls_abc* > wall_density = 144 144 > wall_ewald_zfac= 3 > > > best wishes, > Baofu Qiao > -- Sincerely yours, ** Dr. Baofu Qiao Institute of Computational Physics, University of Stuttgart TEL:+49-711-685 63607 ** -- 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] "Specified frame doesn't exist or file not seekable" when using .xtc
Hi, I am using Gromacs 3.3.1. The .xtc file is obtained from mdrun, as shown in the following ; 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= 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 100 ; Output frequency and precision for xtc file nstxtcout= 10 xtc-precision= 1000 2007/11/1, David van der Spoel <[EMAIL PROTECTED]>: > > Qiao Baofu wrote: > > Hi, all > > > > When I using the .xtc file to analyse, I always meet the following error > > information > > Specified frame doesn't exist or file not seekable > > While it works when using the .trr file. In analyzing, only the > > coordinate is used. Therefore, I want to use .xtc file. In this way, it > > runs a little faster. However, the above proble exits. What's wrong > > with the .xtc file? and how to solve it? > > > gmx version please. > > Thanks! > > > > -- > > Sincerely yours, > > Dr. Baofu Qiao > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Sincerely yours, ** Dr. Baofu Qiao Frankfurt Institute for Advanced Studies Johann Wolfgang Goethe University Ruth-Moufang Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-79847522 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] "Specified frame doesn't exist or file not seekable" when using .xtc
Hi, all When I using the .xtc file to analyse, I always meet the following error information Specified frame doesn't exist or file not seekable While it works when using the .trr file. In analyzing, only the coordinate is used. Therefore, I want to use .xtc file. In this way, it runs a little faster. However, the above proble exits. What's wrong with the .xtc file? and how to solve it? Thanks! -- Sincerely yours, Dr. Baofu Qiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about the total-energy of energy minimization
Hi all, I run an energy minization, then calculated the energy, obtained the following results: LJ-(SR)-4431.621905.29 1886.7 -27.08 - 919.923 Coulomb-(SR) -35926.514398.414389.9 -50.5129 -1715.95 Potential -46818.120524.520248.7-341.91 - 11614.9 Kinetic-En. 0 0 0 0 0 Total-Energy 0 0 0 0 0 Temperature 0 0 0 0 0 Why the Total-energy is not the sum of Potential and Kinetic-En.? Thanks! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_sdf again
2007/3/29, Dallas B. Warren <[EMAIL PROTECTED]>: Syma, > I am using g_sdf to calculating the spatial distribution of > lipid headgroups around other species in my system. > > The thing is when I get the gro file (produced by using the -r flag in > g_sdf) and then look at this in vmd or chimera with my > spatial density file (plt), the reference gro file is not > positioned 'in' the box of density produced by g_sdf. > > Is this as it should be and I am interpreting my results > incorrectly, or have I set up my coordinate system incorrectly? That does sound a bit unusual. However, I use g_sdf quite extensively but don't use the reference structure function. Reason for this, is I have found that the one generated for the molecules I simulate it is highly distorted and the corresponding atom locations do not match up with where they they are located if you calculate the sdf for the non-coordinate atoms within the molecule. Yes. I also found that. Because I want to use the COM of the reference group to calculate the sdf, and the problem of "-r" flag, I rewrite this program. It works. But it seems my program always uses too much memory. Who can give some suggestions to save the memory? Thanks a lot! So I use a representative molecule, rotate to match the sdf for atoms within the molecule, then use that. Not the best way to do it, but it gets what I need. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rdf normalisation
2007/3/26, syma <[EMAIL PROTECTED]>: Hi, I am attempting to calculate the rdfs of the various components of my system wrt to DNA phosphate groups. However, I was wondering how I can normalise so I can compare the various rdfs? Ideally I would like to have the g(r) normalised in the range 0-1. In fact, there is not flag to control the normalised range. But you can take the range, 0-1, of rdf.xvg. The caluclated neighbour number at dr is normalised by the ideal case at dr (average density times the volume at dr) . For the ideal condition, the density at the short range is the same as the average density. Therefore, .. I have read on the user list that I should get three columns in the *.xvg output, the distance, the normalised data and the raw data, I only get two columns. The default rdf.xvg will give only two columns, r and g(r) Thanks in advance for any help. -Syma *** Dr Syma Khalid Department of Biochemistry, University of Oxford South Parks Road, Oxford OX1 3QU U.K. *** ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] coordination number of ion: rdf integration
2007/3/16, andrea spitaleri <[EMAIL PROTECTED]>:
Qiao Baofu wrote:
>
> When integrating, it is for the sphere: 4*PI*integral[/pho*r^{2}*dr].
fine. this is clear, where rho = N/V and N = number of particles (7 ions
in this case)
and V is the total Volume.
N is the total number of the atoms to be calculated (the 2nd group in the
input of g_rdf) in your system.
Therefore, the efficient volume is (10x10x10). this may give you N=6.
why the efficient volume should be 10x10x10? I cannot figure out how did
you retrieve this conclusion.
When calculatin the rdf, half of the shortest box length is used to
determine how long distance will be calculated. You can see that from the
code of gmx_rdf.c.
Thanks for your help anyway,
Regards
Andrea
--
---
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Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
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Frankfurt Institute for Advanced Studies
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Re: [gmx-users] coordination number of ion: rdf integration
2007/3/16, [EMAIL PROTECTED] <[EMAIL PROTECTED]>:
Hi all,
I am struggling with the rdf. I have 7 structural ions in my protein and
I'd like to monitor the coordination number around them (ion - protein)
during my MD. I have read papers about it and:
http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html
and
http://www.gromacs.org/pipermail/gmx-users/2006-November/024694.html
and
http://www.gromacs.org/pipermail/gmx-users/2003-August/006621.html
and trying to get my conclusions.
If I use xmgrace to visualize rdf.xvg and I integrate from 0 to the
first minimum (trapezoid method) I get 6 wich matches the number of
rdf_cn.xvg (obtained by the -cn option) and mainly matches the right
coordination number around my ion.
However if I try to use the method explained in:
http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html
I get a total different results (0.013) using V = (12x11x10)nm3 and N=7.
What am I doing wrong? Did I misunderstand something (probably yes...)?
Something that may be helpful.
When integrating, it is for the sphere: 4*PI*integral[/pho*r^{2}*dr].
Therefore, the efficient volume is (10x10x10). this may give you N=6.
Thanks for any clarification.
Regards,
andrea
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria")
il codice fiscale della
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
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Sincerely yours,
**
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**
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Re: [gmx-users] How to calculate angle dependent rdf
Do you mean SDF, which has been implement by different workers? Or you can rewrite it according to your aim. 2007/3/12, 齐文鹏 <[EMAIL PROTECTED]>: Dear everyone, I read it from the 3.3 manual that the g_rdf program can calculate the angle dependent rdf. But I cannot find how to implement it ? Which option should be chosen? Could anyone help me? Thank you !! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PME, epsilon_rf and dielectric constant calculation
2007/3/8, Itamar Kass <[EMAIL PROTECTED]>: Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using PME, if it important, what it should be? 2. Whet is the best way to calculate the dielectric constant of the simulation box, does g_dipole is enough or should I use g_dielectric also. g_dipole is to calculate the static dielectric constant, g_dielectric is to calculate the frenquency-dependent dielectric constant. Best, Itamar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rdf
2007/3/7, marco cammarata <[EMAIL PROTECTED]>: Hi, I'm using g_rdf to calculate the RDF of a system. The "r range" ends at 3nm. r range ends at 3nm because (your box size)/2 is 3 nm I would like to change it to 100nm but it seems that there are no option for it. 100 nm? Are you sure? it is much biggger than your box size, so you will have some pairs between an atom and itself (in other boxs). If you really want so, you can change some lines in the gmx_rdf.c. Can you help me ? thanks, marco -- Marco Cammarata, Post-Doc European Synchrotron Radiation Facility Material Science Group 6, rue Jules Horowitz BP 220, Grenoble Cedex 38043, FRANCE Beamline ID09b Office : +33 (0)4 76 88 29 37 Beamline : +33 (0)4 76 88 26 95 Fax : +33 (0)4 76 88 27 43 email: [EMAIL PROTECTED] http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID09B/ http://www.fisica.unipa.it/~emoglobina/marco ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] positive system total-energy
Hi David, Thanks for your reply! It is a pure ionic liquid system. I compared this energy result with that of another system, found that the term of "Coul.-recip." is very smaller (- 4664.24) than another system's result (-56014.1). All other terms of the energy are in the same order of magnitute. What does Coul.-recip mean? PME is used for Coulomb interaction. Switch is used for LJ interaction. 1. abnormal result Energy Average RMSD Fluct. Drift Tot-Drift --- Bond8121.16129.568129.564 0.000320592 3.20592 Angle 16284.9174.598174.578 -0.00090818- 9.0818 Ryckaert-Bell. 4489.18147.842144.019 -0.0115717 -115.717 LJ-141169.9734.081833.9909 -0.000861911 - 8.61912 Coulomb-14 2666.03191.396186.964 -0.0141849 -141.849 LJ-(SR)-32381.8146.511 146.4 -0.0019765- 19.765 Disper.-corr. -2462.415.292795.28651 8.934e-05 0.8934 Coulomb-(SR) -11046.1213.609210.484 0.0126112126.112 Coul.-recip. -4664.24 141.26136.108 0.0130948 130.948 Potential -17823.3250.663250.472 -0.00338716 - 33.8716 Kinetic-En.32678.4188.545188.545 -6.01562e-06 - 0.0601562 Total-Energy 14855.1163.416163.122 -0.00339318 - 33.9318 Temperature299.9651.730711.73071 0 0 2.normal results Energy Average RMSD Fluct. Drift Tot-Drift --- Bond3707.66103.252103.238 0.000572337 5.7156 Angle 10644.9157.095157.095 4.14791e-06 0.0414228 Ryckaert-Bell. 3215.44108.937108.932 -0.000366312 - 3.65815 LJ-14 1314.1929.530329.5302 -3.01152e-05 - 0.300743 Coulomb-14 -14049.817.410417.4061 0.0001343981.34216 LJ-(SR)-11648.8158.786 158.35 0.00408289 40.7735 Disper.-corr. -1192.913.766083.73988 0.000153815 1.53606 Coulomb-(SR) -31913.4149.436148.956 0.004152841.4716 Coul.-recip. -56014.136.376436.0691 0.00163665 16.3442 Potential -95936.8248.465 246.67 0.0103406 103.266 Kinetic-En.23457.6186.095186.095 1.29671e-05 0.129495 Total-Energy -72479.2162.228159.458 0.0103536 103.395 Temperature 399.9283.172723.17272 2.21097e-07 0.00220797 2007/3/6, David van der Spoel <[EMAIL PROTECTED]>: Qiao Baofu wrote: > Hi, > > I have a 10 ns job. But when using the g_energy to calculate the > component of the energy, I got a positive total-energy!! > > Who can give some suggestions? Thanks a lot! > what kind of system? do you happen to have an organic solvent? in that case you should subtract the self energy per molecule -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] positive system total-energy
Hi, I have a 10 ns job. But when using the g_energy to calculate the component of the energy, I got a positive total-energy!! Who can give some suggestions? Thanks a lot! The NTP ensemble is used. Before the final run, it has been run for 2ns to get the equilibrium state. The system has about 1 atoms. As shown in the following, the rmsd of the total energy and density are not quite big. Energy Average RMSD Fluct. Drift Tot-Drift --- Bond8121.16129.568129.564 0.000320592 3.20592 Angle 16284.9174.598174.578 -0.00090818- 9.0818 Ryckaert-Bell. 4489.18147.842144.019 -0.0115717 - 115.717 LJ-14 1169.9734.081833.9909 -0.000861911 - 8.61912 Coulomb-14 2666.03191.396186.964 -0.0141849 - 141.849 LJ-(SR)-32381.8146.511 146.4 -0.0019765- 19.765 Disper.-corr. -2462.415.292795.28651 8.934e-05 0.8934 Coulomb-(SR) -11046.1213.609210.484 0.0126112 126.112 Coul.-recip. -4664.24 141.26136.108 0.0130948 130.948 Potential -17823.3250.663250.472 -0.00338716 - 33.8716 Kinetic-En. 32678.4188.545188.545 -6.01562e-06 - 0.0601562 Total-Energy14855.1163.416163.122 -0.00339318 - 33.9318 Temperature 299.9651.730711.73071 0 0 Pressure-(bar) 1.02259336.285336.285 -5.31626e-06 - 0.0531626 Density-(SI)1583.313.403233.39918 -5.7445e-05 - 0.57445 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protein Dipole moment
no. the com is not used in the g_dipoles.
The simplest way to use com is to replace the content of the { void
mol_dip() } with the following code.
int k,kk,l;
real q,m,m_sum,q_sum;
q_sum = 0;
m_sum = 0;
for(k=k0; (k:
Hello
Does g_dipole take the center of mass of a molecule as the origin when
calculates its dipole moment?
If yes, is it the com at t=0 that is used or is it re-calculated for every
frame?
I had look at the source code but it wasn't very clear to me.
Thank you very much in advance.
Best wishes
George
Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK
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--
Sincerely yours,
**
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**
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[gmx-users] question about genbox -vdwd
Hi all, I have one question: when I use the "genbox -nmol 300 -ci a.gro -cp b.gro" to insert a.gro into b.gro, for some system it gives good results, while not for others. On the other hand, the -vdwd opinion seems not work. I looked at the code of gmx_genbox.c, but didn't find the reason. From the google, I found the following. The problem is the same as mine. Who has good suggestions? Thanks in advance! === http://www.gromacs.org/pipermail/gmx-users/2004-August/011926.html *The resulting output contains atoms which are too close. The distance *>*between the atoms is sometimes *>*as small as 0.01 nm which is smaller than the vanderwaals radii from the *>*database vdwradii.dat . Not *>*surprisingly, therefore I get errors when I run energy minimization or mdrun. *>* The output keeps repeating the message "tested 0 pairs, removed 0 atoms *>* " as I quote below. I would *>*greatly appreciate if somebody could guide me how to use genbox properly. * genbox isn't that good at randomly placing molecules within a box in cases like this (are some emails in the archive on this). It needs a bit of work. I use an in house program to do it, works out much better. Although I don't have it to give out to anyone, since it is part of a much larger package that does a lot of other things and isn't mine to make available. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] loss of information trr xtc
If I understand correctly, only the coordinate information can be saved in .xtc. That means, all other informations, velocity, force, etc, can't be reconverted into .trr again. 2007/2/9, Joern Lenz <[EMAIL PROTECTED]>: hi guys. can anyone tell me if there is a loss of information when i convert a trr file into a less-storage-consuming xtc file ? can i reconevrt the xtc file into trr again and then have no loss of information ? thanks for a very short answer Greetings Joern ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: fudgeQQ (again ...) and fudgeLJ
Hi, I have just tested the fudgeQQ and fudgeLJ, and found one problem: I use the ffoplsaa force field, and add the atoms I used.(in the ffolpsaanb.itp file, there is no [pairtype] section, and I only add the atom informations: ; name bond_typemasscharge ptype sigma epsilon opls_966 CT 6 12.01100 0 A3.4e-01 4.5770e-01) I write my .itp file by hand, in which in the [ pairs] section, I write the pairs and the function, but don't give the values of C6 and C12, that is, [ pairs ] ; ai aj fuc6c12 15 1 16 1 ... In the ffoplsaa.itp, I used ; nbfunc comb-rulegen-pairsfudgeLJ fudgeQQ 1 2yes 0.5 0.8333 I used different values of fudgeLJ and fudgeQQ in the 4 tests, see the following fudgeLJfudgeQQ result (from .log file): LJ-14Coulomb-14 1. 0.5 0.5 1.48e+02-8.896e+03 2 11 1.96e+02-1.793e+04 3.0.250.25 9.58e+01-4.43e+03 4. 0.50.8333 1.96e+02 -1.498e+04 The problem is that the LJ-14 doesn't change with the scaling factor of fudgeLJ. Why? Does it mean that I must give the C6 and C12 in the .itp file? If yes, should the C6 and C12 scaled by the scaling factor (0.5) and "gen-pairs = no; fudgeLJ=1" ? Another question is that in the .log file, what is the "Disper. corr."? What is the difference between it and the 1-4 interacion? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: fudgeQQ (again ...)
2006/12/7, [EMAIL PROTECTED] <[EMAIL PROTECTED]>: By the way, why are you using the combination of genpairs=yes fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for any force field that comes in the standard gromacs distribution. Hi, I am puzzled about this. In your opinion, when I use genpairs=no, fudgeLJ= 0.5 and fudgeQQ=0.8333, are these scaling factors, 0.5 and 0.8333, useful? On the other hand, when using genpairs=yes, how to set the scaling factor of fudgeLJ and fudgeQQ?$ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] strange NTP trajectory
Hi all, I run NTV firstly for 100ps, then change to NTP for 1ns. The mdrun finished with the common informations. But when I use vmd (or ngmx) to look at the trajectory, I found that during the NTP stage, starting from 100ps, all the molecules don't move except only one molecules. The output file .gro of NTP seems ok. Who knows the reason? Sincerely yours, Baofu Qiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to get a equilibriumed system effectively
Hi all, Now I meet a problem when building a system. I used prodrg to get the .pdb of a single molecule, write the .top file manually. The single-molecule system is equilibriumed (em, NVE, NTV,NTP are all ok for at least 1 ns). Then I used two method to get a bigger (8 molecules) system: 1) genbox -cs -box; 2) genbox -nmol -ci -cp. Both result are ok when EM. But when NVE is runn, result 2 crashed right now . For results 1, NVE is ok, and short-time NTV and NTP(about 10ps) are ok, but long-time NTV and NTP(1ns) crashed with the same reason. On the other hand, I build a very dilute sytem (5 molecules, density is about 2 g/l). It runs very well. But the problem is it is very hard to converge to the suitable density (1000 g/l). Who knows how to solve it? Thanks a lot. Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 1000 ] Please report this to the mailing list (gmx-users@gromacs.org) --- -- Baofu Qiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] radial distribution function
To my knowledge, g_rdf calculate all the atoms of group A to all the atoms of group B to get the gAB(r). g_rdf -com calculate the center of group A, not the centers of the residues in group A to all the atoms of group B. I upload a file based on gmx_rdf.c to calculate the centers of residues of group A (and B) last month to the website of gromacs. 2006/11/22, Nguyen Hoang Phuong <[EMAIL PROTECTED]>: My question is that how does gromacs compute g(r)? Is r the distance between center of mass of the group [ Pep ] and the center of mass of each solvent molecule? Or gromacs computes g_i(r) between each atom of the group [ Pep] with respect to solvent molecules and then take average over all g_i(r) to get g(r)? Many thanks in advance, Phuong ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Baofu Qiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to simulate at a specific dielectric constant
Hi David,There is not a simulation parameter that you can change that will influence the dielectric constant of your system. I don't grasp this. If the system has two fluid, one as solute, another as solvent. I had thought that I should change the value epsilon_r in the .mdp file from the default 1 to some other value. Is it wrong? --David.-- Sincerely yours, **Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to simulate at a specific dielectric constant
yes. In the .mdp, epsilon_r gives the relative permittivity of the medium2006/11/15, Mark Abraham <[EMAIL PROTECTED]>: > Dear all> How can i set the dielectric constant of my choice in the simulationsPlease read the manual.Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] calculating dielectric constant
Hi David, Thanks for your kindly reply.Because I am simulating a pure fluid system, I used the epsilon-r = 1in the .mdp file. _ coulombtype = pme rcoulomb-switch = 0 rcoulomb = 1.1 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 _ If I don't use the Reaction-Field method, how should I use the -rpsilonRF option? (I want to use 0. But because 0 means infinity here, I have no idea how to use it) I calculated dielectric constant with and without "-esilonRF" option, please see the following results _g_dipoles -temp 425 -f md2 -s md2 -enx md2.edrEpsilon = 826.496g_dipoles -temp 425 -epsilonRF 1 -f md2 -s md2 -enx md2.edrEpsilon = -2.01094 _Neither result are the values what I expect. What wrong?2006/11/13, David van der Spoel < [EMAIL PROTECTED]>: Qiao Baofu wrote:> Hi all,>> I have some question about calculating dielectric constant:> 1. From the manual, it seems that there are two methods to calculate the> dielectric constant: a. use g_dipoles -temp 400 -f -s directly, b) use > g_dipoles -nonormalize -corr total -c dipcorr.xvg, then g_dielectric -f> dipcorr.xvg -o epsw.xvg. (Please correct me if the commandlines are> wrong). Thus I want to know the difference between them. g_dielectric does another analyis. You want to run g_dipoles either withthe -enx flag or with a trajectory.> 2. If I want to calculate the dielectric constant, must I use the> Reaction Field in the couloumbtype? Now I have some results from PME. > Can I use these results directly to calculate the dielectric constant?PME is fine. You have to supply the right dielectric constant to theprogram (though the default of 0 == infinity) is what most people use. >> Thanks very much in advances!>>>> Sincerely yours, > Baofu Qiao>>> --David. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] calculating dielectric constant
Hi all,I have some question about calculating dielectric constant:1. From the manual, it seems that there are two methods to calculate the dielectric constant: a. use g_dipoles -temp 400 -f -s directly, b) use g_dipoles -nonormalize -corr total -c dipcorr.xvg, then g_dielectric -f dipcorr.xvg -o epsw.xvg. (Please correct me if the commandlines are wrong). Thus I want to know the difference between them.2. If I want to calculate the dielectric constant, must I use the Reaction Field in the couloumbtype? Now I have some results from PME. Can I use these results directly to calculate the dielectric constant? Thanks very much in advances!Sincerely yours,Baofu Qiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about energy fluctuation
I did again two group of tests, as follows. But I don't know how to submit a bugzilla.Test 1.g_energy -f md3.edrEnergy Average RMSD Fluct. Drift Tot-Drift ---Bond 1370.47 64.952 64.8116 0.0295732 14.7866Angle 3541.69 99.9164 99.9059 0.0100593 5.02964LJ-(SR) -3601.66 151.232 131.574 -0.516572 -258.287Coulomb-(SR) -10883 143.406 134.139 -0.351347 -175.674Potential -30962.9 304.081 265.607 -1.0257 -512.85Total-Energy -22436.1 287.863 245.635 -1.03989 -519.945g_energy -nmol 115 -f md3.edrEnergy Average RMSD Fluct. Drift Tot-Drift ---Bond 11.9171 0.5648 0 0.0295732 14.7866Angle 30.7973 0.868838 0 0.0100593 5.02964LJ-(SR) -3601.66 151.232 131.574 -0.516572 -258.287Coulomb-(SR) -10883 143.406 134.139 -0.351347 -175.674Potential -269.242 2.64418 0 -1.0257 -512.85Total-Energy -22436.1 287.863 245.635 -1.03989 -519.945Test 2.g_energy -f md3.edrEnergy Average RMSD Fluct. Drift Tot-Drift---Bond 27255.4 288.517 287.731 0.147486 73.7433Angle 30206.8 299.196 299.151 -0.0361126 -18.0563LJ-(SR) -27021.1 1153.88 1015.89 -3.7911 -1895.55Coulomb-(SR) -116585 1327.11 1120.39 -4.92805 -2464.03Potential -271448 2889.94 2444.54 -10.6792 -5339.61Total-Energy -183054 2912.13 2478.91 -10.588 -5293.99g_energy -nmol 981 -f md3.edrEnergy Average RMSD Fluct. Drift Tot-Drift---Bond 27.7833 0.294105 0 0.147486 73.7433Angle 30.7919 0.304991 0 -0.0361126 -18.0563LJ-(SR) -27021.1 1153.88 1015.89 -3.7911 -1895.55Coulomb-(SR) -116585 1327.11 1120.39 -4.92805 -2464.03Potential -276.705 2.94591 0 -10.6792 -5339.61Total-Energy -183054 2912.13 2478.91 -10.588 -5293.99 2006/11/9, David van der Spoel <[EMAIL PROTECTED]>: Qiao Baofu wrote:> Thanks.>>>> but the g_energy -nmol can only give the Bond,Angle data divided by the> nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy > -nmol 981 gives the same result as without -nmol 981, in which 981 is> the number of molecules.>> I am using Gromacs 3.3.1.>If this is reproducible then please submit a bugzilla. --David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about energy fluctuation
Thanks. but the g_energy -nmol can only give the Bond,Angle data divided by the nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy -nmol 981 gives the same result as without -nmol 981, in which 981 is the number of molecules.I am using Gromacs 3.3.1. You can divide by the number of molecules using g_energy -nmol. The reason GROMACS doesn't do it for you is that it is well defined onlyfor monomolecular systems. The energy you get is hence kJ/mol system.Where system is your complete system, be it 125 argon atoms or a large biological complex.>> Mark> ___> gmx-users mailing listgmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the www> interface or send it to [EMAIL PROTECTED] .> Can't post? Read http://www.gromacs.org/mailing_lists/users.php--David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies Max-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about energy fluctuation
Hi all,After running a MD of a system with about 17000 atoms, I calculated the potential and the total-energy:*Last frame read 1557952 time 1557.952Statistics over 1557953 steps [ 0. thru 1557.9520 ps ], 2 data setsEnergy Average RMSD Fluct. Drift Tot-Drift--- Potential -273047 626.559 611.258 -0.305998 -476.731Total-Energy -184656 839.662 828.307 -0.305999 -476.731* I found that the Fluct./Average is 0.45% (Total-Energy), 0.22%(Potential). In the simulation, the time step is 0.001ps, and I saved the energy every step. On the other hand, on page 98 of the book "Computer Simulation of Liquids" (M. P. Allen & D. J. Tildesley), it is said "For a simple Lennard-Jones system, fluctuation of order 1 part in 10^4 are generally considered to be acceptable." The ratio obtained from Gromacs are quite bigger. Therefore, I want to know if there are any standard for different system to check whether the system are accetable or not.PS: Another question: I found only when the energy data are divided by the number of the molecules, the obtained result are consistent with the date in some related papers. In Gromacs, the unit of energy is KJ/mol. If divided by the number of molecules, how to consider the unit? Thanks for any suggestions!Sincerely yours,Baofu Qiao, PhD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in compiling g_velacc again under gromacs
Hi,I compile it again in the source folder ~/src/tool/ and the installation folder ~/gromacs/bin. It give the same complains.What can I do?2006/10/31, Mark Abraham < [EMAIL PROTECTED]>:Qiao Baofu wrote: > Hi all,>> I want to comile the g_velacc again. I copy the original gmx_velacc.c> and autocorr.c into a new directory, and then comile the gmx_velacc.c,> but it gives the following complains, and then exits. (I didn't change > anything in the two files!!) How to solve it? Thanks a lot.Does it work if you do it in the same directory? That's got to be cleaner...Mark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in compiling g_velacc again under gromacs
I think the problem is because I compile Gromacs under 64-bite model. the g_velacc.c can not be recognized under 64 bite model.But when I compile it under 32-bite it gives the following complains. On the other hand I am not sure whether a file (which is ok under 32-bite system ) can be copied to 64-bite system. /usr/bin/ld: skipping incompatible /home/fias/qiao/Gromacs//lib/libmd.a when searching for -lmd/usr/bin/ld: skipping incompatible /home/fias/qiao/Gromacs//lib/libmd.a when searching for -lmd/usr/bin/ld: cannot find -lmd collect2: ld returned 1 exit status2006/10/31, Qiao Baofu <[EMAIL PROTECTED]>: Hi,I compile it again in the source folder ~/src/tool/ and the installation folder ~/gromacs/bin. It give the same complains.What can I do?2006/10/31, Mark Abraham < [EMAIL PROTECTED]>: Qiao Baofu wrote: > Hi all,>> I want to comile the g_velacc again. I copy the original gmx_velacc.c> and autocorr.c into a new directory, and then comile the gmx_velacc.c,> but it gives the following complains, and then exits. (I didn't change > anything in the two files!!) How to solve it? Thanks a lot.Does it work if you do it in the same directory? That's got to be cleaner...Mark___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies Max-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in compiling g_velacc again under gromacs
Hi all,I want to comile the g_velacc again. I copy the original gmx_velacc.c and autocorr.c into a new directory, and then comile the gmx_velacc.c, but it gives the following complains, and then exits. (I didn't change anything in the two files!!) How to solve it? Thanks a lot.
**/home/fias/qiao/Gromacs//lib/libgmxana.a(autocorr.o)(.text+0x22b0): In function `low_do_autocorr':: undefined reference to `xvgropen'
/home/fias/qiao/Gromacs//lib/libgmxana.a(autocorr.o)(.text+0x2e83): In function `low_do_autocorr':: undefined reference to `xvgropen'/home/fias/qiao/Gromacs//lib/libgmxana.a(expfit.o)(.text+0x6cb): In function `do_lmfit':
: undefined reference to `xvgropen'collect2: ld returned 1 exit status**The following are used to compile it:
GMXDIR='/home/fias/qiao/Gromacs/'INCLUDE="-I${GMXDIR}/include/gromacs -I${GMXDIR}/include/gromacs/types"LIBS="-L${GMXDIR}/lib -L/usr/X11R6/lib -L/lib -L/usr/lib -L${GMXDIR}/lib"LDDFLAGS="-lXm -lmd -lm -lgmx -lgmxana -lnsl -lfftw3"
CCFLAGS="-O3"gcc -g $INCLUDE $CCFLAGS -c gmx_velacc.cgcc -g $CCFLAGS -o g_velacc gmx_velacc.o -Wall $LIBS $LDDFLAGS**
-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**
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[gmx-users] question about calculation electrical conductivity with green-kubo relation
Hi all,I wrote a program to calculate the electrical conductivity at zero field using the Green-Kubo relation, as follows. But I found the calculated data are strange: in the first stage, the data are very big, while in the end stage it is a negative value, also quite big. (I used the system with about 3500 atoms, 4 ns (every 100 ns are taken as one ensemble).
Is there anyone who can give some suggestions? Thanks.#ifdef HAVE_CONFIG_H#include #endif#include #include #include "
confio.h"#include "copyrite.h"#include "fatal.h"#include "futil.h"#include "gstat.h"#include "macros.h"#include "maths.h"#include "
physics.h"#include "index.h"#include "smalloc.h"#include "statutil.h"#include "string.h"#include "sysstuff.h"#include "txtdump.h"
#include "typedefs.h"#include "vec.h"#include "strdb.h"#include "xvgr.h"int main(int argc,char *argv[]){ static char *desc[] = { "This program is wroten to calculate the Electrcal Conductivity.",
"The Green-Kubo relation is used. See the reference:", "J-P Hansen, I. R. McDonald: Theory for Simple Liquids, 2nd Edition, P242." }; t_pargs pa[] = { }; #define NPA asize(pa)
t_filenm fnm[] = { { efTRX, "-f", NULL, ffREAD }, { efTPX, "-s", NULL, ffREAD }, { efNDX, "-n", NULL, ffOPTRD }, { efXVG, "-o", "EC", ffWRITE }
};#define NFILE asize(fnm) FILE *fp_EC; t_topology top; t_trxframe fr; bool bTop=FALSE; int gnx; atom_id *index; char *grpname; char title[256];
real q,t,t0; int status,i,j; real *qv,*qv0; int i_T_N,T_N=10,Ensemble_N; real *Integrand,*Integral,EC; real T_fac; real kb=1.381e-23,e=1.6e-19
,v_c=1e3,t_c=1e-12; //v_c: the coefficient between nm/ps and m/s real T=425,V=47.3,Pref; // Temperature, Volume and Prefacor //printf("\nPlease input the Temperature(K) and Volume(nm^3),\n& How many data points per ensemble:\n");
//scanf("%f %f %g",&T,&V,&T_N); V=V*1.0e-27; Pref = 1.0/(kb*T)*(e*v_c)*(e*v_c)*t_c/V; printf("Prefactor = %10g\n", Pref); printf("\n");
//CopyRight(stderr,argv[0]); parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL); bTop=read_tps_conf(ftp2fn(efTPX,NFILE,fnm),title,&top,NULL,NULL,NULL,TRUE);
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname); sprintf(title,"Electrical Conductivity: %s",grpname); fp_EC=xvgropen(opt2fn("-o",NFILE,fnm),title,"t (ps)","EC (S/m)");
snew(qv0,DIM); snew(qv,DIM); snew(Integrand,T_N); snew(Integral,T_N); read_first_frame(&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_NEED_V); for(i=0; i Integral[i]=0;
Ensemble_N=0; EC=0; next_ensemble: t0=fr.time; for(i=0; i qv0[i]=0; for(i=0; i q = top.atoms.atom[index[i]].q; qv0[0] += q*
fr.v[index[i]][XX]; qv0[1] += q*fr.v[index[i]][YY]; qv0[2] += q*fr.v[index[i]][ZZ]; } i_T_N = 0; do { t=fr.time; for(i=0; i qv[i]=0; for(i=0; i q = top.atoms.atom[index[i]].q; qv[0] += q*fr.v[index[i]][XX]; qv[1] += q*fr.v[index[i]][YY]; qv[2] += q*fr.v[index[i]][ZZ]; } Integrand[i_T_N] = qv[0]*qv0[0]+qv[1]*qv0[1]+qv[2]*qv0[2];
// T_fac is the factor between time and i_T_N if(i_T_N==(T_N-1)) T_fac = (t-t0)/i_T_N; i_T_N++; if (i_T_N == T_N) { for (j=0; j Integral[j] += Integrand[j];
Ensemble_N++; if (read_next_frame(status,&fr)) goto next_ensemble; } } while (read_next_frame(status,&fr)); close_trj(status); for (i=0; i { EC += Pref*Integral[i]/Ensemble_N*T_fac; fprintf(fp_EC, "%7.3f %10g \n",i*T_fac,EC); } ffclose(fp_EC); thanx(stderr); return 0;}-- Sincerely yours,**
Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529**
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Re: [gmx-users] strange new H-H bond formation during MD
Thanks.I check the animation of VMD again, and found that during the animation, some H-H connections are displayed. But as the time grow, they disappear sooner or later. On the other hand, the mdrun didn't crash for 500 ps ( 0.001ps/step). Therefore, I think it is the problem of the display of VMD. I used the g_mindist to calculate the minimal distance of all the hydrogens (Firstly I select all the hydrogens as one group in make_ndx, then use only this group in g_mindist ), found that generally it is bigger than 0.12nm, but there is one strange point, it is about 0.1 nm (0.0995nm). Therefore, 1) it is true that there are some short H-H distances during the MD, 2) the mdrun is ok. I think I can trust the result of mdrun, but I need a longer mdrun. Thanks for all!!2006/10/24, Mark Abraham <[EMAIL PROTECTED]>: Well the URL I provided above omits PDB files from the list of filetypes that VMD reads for bond connectivity. Hence I suspect Baofu hasmisinterpreted something, or that manual section is incomplete.Mark -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] strange new H-H bond formation during MD
Hi Tsjerk,Yes, you are right!2006/10/24, Tsjerk Wassenaar <[EMAIL PROTECTED]>: Note that it should be CONECT and not CONNECT...Tsjerk-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies Max-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] strange new H-H bond formation during MD
Yes. Gromacs can only generate the .pdb file without CONNECTION. I think it is not only Gromacs but Material Studio that do like that. For more than 2 molecules, the softwares give only the coordinate data. I find a top2psf.tcl file on the website of VMD (Script Library). It is said this script can transfer .top file to .psf file, which can be recognized by VMD. But I don't know how to use it and the website of VMD doesn't give the instrution how to use it. :( 2006/10/24, Erik Marklund <[EMAIL PROTECTED]>: >> PDB files do not contain bond connectivity. By the look of> http://www.ks.uiuc.edu/Research/vmd/current/ug/node21.html, you can't > tell VMD your gromacs connectivity, unless you write your own plug-in to> VMD (hint, hint). You could also try asking the VMD mailing list. Your> simplest plan is likely to be to generate a PSF or PARM file with an > equivalent topology, for they are used in other MD codes to contain the> connectivity.That's not entirely true. Normally, pdb files do not contain topologicalinformation, but they CAN do so through a CONNECT block. This is probably why VMD claims that ".pdb contain the information of bond-connectivity" (don't use vmd myself, just cited Bafou above). However,to my knowledge, gromacs completely ignores CONNECT blocks in pdb output/input, which is why you see atoms only, and no connection.-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies Max-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] strange new H-H bond formation during MD
Thanks. Now I understand what happens.But in the user-manual of VMD, it is said that only four Gromacs file (GRO, G96, XTC, TRR) and .pdb can be read by VMD. But only the .pdb contain the information of bond-connectivity (if I understand correctly). The point is that the output .pdb file from mdrun contains only the coordinate information! How can I tell VMD the bond-connectivity information?!! I used the "mol new myfile.gro autobonds 0" to see my molecules. Unfortunately, only atoms are displayed, no connection. 2006/10/23, Ignacio Fernández Galván < [EMAIL PROTECTED]>:--- Mark Abraham < [EMAIL PROTECTED]> wrote:> Right, so like I said earlier, you're not giving it your topology,> because you're loading from a .gro file. Instead, VMD is making stuff> upIncidentally, you can disable this behaviour by loading the file in VMD with "mol new myfile.gro autobonds 0" (or something like that).Send instant messages to your online friends http://uk.messenger.yahoo.com___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] strange new H-H bond formation during MD
Hi Mark,Thanks for your reply.I used these: 1. vmd em_out.gro 2. use the "load data into molecules...", select md1.trr, and then load 3. when the anmination is finished, I can see some H-H bonds. 2006/10/23, Mark Abraham <[EMAIL PROTECTED]>: > Hi All,>> I meet a problem in run MD: from the display of VMD, there are some H-H> bonds formed during the MD. All the bonds I wrote in .itp file are right,> except these new unexpected H-H bonds. (I generate the system from a > smaller system, EM is ok, when running NTV, the problem comes. ) Who can> give some suggestions? Thanks in advances.Unless you opened the structure from a .tpr file, VMD can't even haveaccessed your topology. It has its own heuristics for deciding whether to show a bond exists. See the VMD documentation for details. Whether theseclose H-H contacts are a problem is for you to judge :-)Mark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] strange new H-H bond formation during MD
Hi All,I meet a problem in run MD: from the display of VMD, there are some H-H bonds formed during the MD. All the bonds I wrote in .itp file are right, except these new unexpected H-H bonds. (I generate the system from a smaller system, EM is ok, when running NTV, the problem comes. ) Who can give some suggestions? Thanks in advances. PS: I have succeeded in simulating a samller system by using the same force-field. So I think the .itp file should be right.-- Sincerely yours,** Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] warning: assignment makes pointer from integer without a cast
Hi David,Thanks a lot.Now, it works.2006/10/19, David van der Spoel <[EMAIL PROTECTED]>:
Qiao Baofu wrote:> Hi all,>> I meet a problem in compiling my program under gromacs: it always give> the information "warning: assignment makes pointer from integer without> a cast". The line refers to the following line with (***). I have tried
> opt2fn_NULL too.>> How to solve it? and can you give some introduction about the opt2fn,> opt2set, etc?>> Thanks in advance!>>> t_filenm fnm[] = {> { efTRX, "-f", NULL, ffREAD },
> { efTPX, "-s", NULL, ffREAD },> { efNDX, "-n", NULL, ffOPTRD },> { efXVG, "-o", "EC", ffOPTWR }> };>> *** fp=xvgropen(opt2fn("-o",NFILE,fnm),title,"t","Integrand");
>>>>> --> Sincerely yours,> **> Baofu Qiao, PhD> Frankfurt Institute for Advanced Studies> Max-von-Laue-Str. 1
> 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529> **>>> >
> ___> gmx-users mailing listgmx-users@gromacs.org>
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.> Can't post? Read http://www.gromacs.org/mailing_lists/users.phpdid you include xvgr.h in your program?--David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se
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http://www.gromacs.org/mailing_lists/users.php-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies
Max-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529**
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[gmx-users] warning: assignment makes pointer from integer without a cast
Hi all,I meet a problem in compiling my program under gromacs: it always give the information "warning: assignment makes pointer from integer without a cast". The line refers to the following line with (***). I have tried opt2fn_NULL too.
How to solve it? and can you give some introduction about the opt2fn, opt2set, etc?Thanks in advance! t_filenm fnm[] = { { efTRX, "-f", NULL, ffREAD }, { efTPX, "-s", NULL, ffREAD },
{ efNDX, "-n", NULL, ffOPTRD }, { efXVG, "-o", "EC", ffOPTWR } };*** fp=xvgropen(opt2fn("-o",NFILE,fnm),title,"t","Integrand");
-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**
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[gmx-users] calcualting viscosity from NEMD
Hi all,I want to calculate the shear viscosity of a small molecule pure fluid. Therefore, I run some non-equilibrate MD. But I don't know what values should be given to "accelerate" and "cos-acceleration". Please see my results below. I found that:1. with the "cos-acceleration" decreasing, 1/viscosity decrease almost continuously, and the rmsd increase.2. The value of "accelerate" doesn't affect 1/viscosity greatly. Thus "accelerate=0.1" is acceptable, but how about the "cos-acceleration"?Who has such experience? Can you give me some suggestions? Thanks in advances!1. md4#accelerate = 0.1 0 0 -0.1 0 0#cos-acceleration = 0.5 Energy Average RMSD Fluct. Drift Tot-Drift --- 2CosZ*Vel-X 0.170636 0.0329107 0.0328585 -6.414e-06 -0.006414 1/Viscosity-(SI) 944.025 183.219 182.931 -0.0355854 -35.58552. md5#accelerate = 0.1 0 0 -0.1 0 0#cos-acceleration = 0.3 Energy Average RMSD Fluct. Drift Tot-Drift --- 2CosZ*Vel-X 0.0323069 0.0181729 0.0180577 7.07857e-06 0.00707858 1/Viscosity-(SI) 294.808 165.922 164.855 0.0650939 65.0943. md6#accelerate = 0.1 0 0 -0.1 0 0#cos-acceleration = 0.1 Energy Average RMSD Fluct. Drift Tot-Drift --- 2CosZ*Vel-X 0.00130712 0.0156865 0.0156829 -1.16341e-06 -0.00116341 1/Viscosity-(SI) 35.5201 426.066 425.967 -0.0316935 -31.69354. md9#accelerate = 0.1 0 0 -0.1 0 0#cos-acceleration = 0.05 Energy Average RMSD Fluct. Drift Tot-Drift --- 2CosZ*Vel-X 0.000350432 0.0149682 0.0149682 -7.67601e-08 -7.67602e-05 1/Viscosity-(SI) 19.0263 812.332 812.331 -0.00409487 -4.094875. md10#accelerate = 0.1 0 0 -0.1 0 0#cos-acceleration = 0.01 Energy Average RMSD Fluct. Drift Tot-Drift --- 2CosZ*Vel-X 0.000121789 0.0152012 0.0152012 0 0 1/Viscosity-(SI) 33.0229 4123.09 4123.09 -0.00116304 -1.163046. md11#accelerate = 0.1 0 0 -0.1 0 0#cos-acceleration = 0.005 Energy Average RMSD Fluct. Drift Tot-Drift --- 2CosZ*Vel-X -4.23371e-05 0.0153689 0.0153689 1.35182e-07 0.000135182 1/Viscosity-(SI) -22.9384 8335.83 8335.8 0.0741577 74.1578*** 7. md7#accelerate = 0.3 0 0 -0.3 0 0#cos-acceleration = 0.1 Energy Average RMSD Fluct. Drift Tot-Drift --- 2CosZ*Vel-X 0.00107554 0.0153412 0.015341 -2.26469e-07 -0.000226469 1/Viscosity-(SI) 29.1877 416.411 416.407 -0.00612827 -6.128288. md8#accelerate = 0.5 0 0 -0.5 0 0#cos-acceleration = 0.1 Energy Average RMSD Fluct. Drift Tot-Drift --- 2CosZ*Vel-X 0.0011791 0.014806 0.0148055 -4.10365e-07 -0.000410365 1/Viscosity-(SI) 32.0258 402.128 402.115 -0.0110667 -11.0667 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about energy and pressure
Hi Mark,2006/9/22, Mark Abraham <[EMAIL PROTECTED]>: Qiao Baofu wrote:What is this "reported data"?The reported data are (KJ/mol) : Bond 27; Angle: 30; LJ: -27; electrostatic -530.Some days ago, I run again in gromacs but using all the "reported" force-field parameters. In the end, I get the similar result as listed in the first letter. Have someone compared the energy of gromacs with other software? > Statistics over 501 steps [ 0. thru 5000. ps ], 6 data sets>> Energy Average RMSD Fluct. Drift> Tot-Drift> --- >> Bond2869.1393.656493.6562 0.000137548> 0.687742> Angle 7303.46 140.13 140.13 0.000189867> 0.949334> Ryckaert-Bell. 3326.297.624597.6161 -0.000890977 -4.45489> LJ-(SR) -7616.62138.684 138.67 -0.00138166> -6.90831> Coulomb-(SR)-22763.2138.465138.238 -0.00549019- 27.451> Potential -64743 219.54219.203 -0.00842365> -42.1182>> 2. I used the "isotropic!!" pressure coupling, but at the end of the> .log file (in the average section), it says: >> Pressure (bar)>-2.64364e+013.71622e+01 3.00738e+00> 3.71622e+011.32932e+01 -2.49814e+01> 3.00738e+00 -2.49814e+011.61609e+01>> The Pxx, Pyy, Pzz are not equal. Why? What is the geometry of your system?It is imidazolium-based material.PS: The following processes are used: 1. md1: NTV (nose-hoover for T coupling) 300ps 2. md2: NTP (Berendsen for T & P coupling) T=425K, P=1bar, 500ps, tau_p=1 3. in md3.mdp: gen_temp = no unconstrained-start = yes grompp -e md2.edr -f md3.mdp -c md2.gro -p -o md3: NTP (nose-hoover for T coupling & Parrillo-rahman for P coupling) T=425K, P=1bar, 3000ps, tau_p=4 4. collect data.g_energy Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure-(bar) 1.75443 931.231 931.227 -0.00331938 -9.95814In md3.log Pressure (bar) 3.37452e+01 -1.01961e+02 1.77413e+01 -1.01961e+02 -7.66155e+00 -4.13047e+01 1.77413e+01 -4.13047e+01 -2.08203e+01Even though I used the Berendsen P coupling to relax the pressure firstly, and then use the Parrilo-rahman, the final result of pressure deviates much from what I want! After md2 and md3, I both used g_velacc to check the velocity-corelation function. Who has such experience? How to solve it? Mark___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about energy and pressure
Hi Dallas Warren,1. The molecules are the same. But we built the system in different method, and used different number of molecules. 2. We both used the oplsaa all-atom force field, but the parameters are a little different. 3. I used gromacs. The reference used MDynaMix.4. The unit of energy are both KJ/molI think no matter what softwares or systems, the energies should almost the same. At least, they should not deviate to much? is it right? PS: For the pressure, I used Berendsen pressure coupling.2006/9/21, Dallas B. Warren <[EMAIL PROTECTED] >:>1. I simualted a pure small molecule system. All the simulation is ok.But >when I use g_energy to calculate the energy of bond, angle, lj, andcoloumb,>it gives the following energy. The energies is much bigger, about50-100 times>bigger than the reported data. What's wrong? Well, that depends on what the reported data actually is to whether youcan actually make the comparison.Is it for exactly the same system with the same forcefield?Is it for the entire system or for per molecule? Catch ya,Dr. Dallas WarrenLecturerDepartment of Pharmaceutical Biology and PharmacologyVictorian College of Pharmacy, Monash University381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED]+61 3 9903 9524-When the only tool you own is a hammer, every problem begins to resemblea nail.___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] 1-4 columb interaction
In the force field file ff***.itp, there are two terms to scale lj and coloumb after the option: generating pairs.2006/9/20, Alok <[EMAIL PROTECTED] >: Dear All, Is there any scaling for 1-4 columb interaction in gromacs force field if yes then how? is it also like LJ14 which uses separate set of parameters for 1-4 interaction? Manual only talked about separate parameters for LJ14 specifically for repulsion term, but in mailing list it was mentioned that there is always scaling for Columb-14 but how I am not able to get? Regards, Alok ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about energy and pressure
Hi all,I have some questions about the gromacs:1. I simualted a pure small molecule system. All the simulation is ok. But when I use g_energy to calculate the energy of bond, angle, lj, and coloumb, it gives the following energy. The energies is much bigger, about 50-100 times bigger than the reported data. What's wrong? Statistics over 501 steps [ 0. thru 5000. ps ], 6 data setsEnergy Average RMSD Fluct. Drift Tot-Drift--- Bond 2869.13 93.6564 93.6562 0.000137548 0.687742Angle 7303.46 140.13 140.13 0.000189867 0.949334Ryckaert-Bell. 3326.2 97.6245 97.6161 -0.000890977 -4.45489LJ-(SR) -7616.62 138.684 138.67 -0.00138166 -6.90831Coulomb-(SR) -22763.2 138.465 138.238 -0.00549019 -27.451Potential -64743 219.54 219.203 -0.00842365 -42.11822. I used the "isotropic!!" pressure coupling, but at the end of the .log file (in the average section), it says: Pressure (bar) -2.64364e+01 3.71622e+01 3.00738e+00 3.71622e+01 1.32932e+01 -2.49814e+01 3.00738e+00 -2.49814e+01 1.61609e+01The Pxx, Pyy, Pzz are not equal. Why?Sincerely yours,** Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs install question
Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory of gromacs 3. ./configure 4. make 5 make install The result is that only the following commands are installed in /bin directory of gromacs: ffscan, gmxcheck, gmxdump, grompp,luck, mdrun, pdb2gmx,protonate,tpbconv, x2top. What wrong with it? who can tell me? Thanks in advance! -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: question about g_rdf -com & a little mistake on make_ndx
Hi,I am using Gromacs 3.3.1. In the help file of make_ndx, it is said that "splitres" is to split group into residues, and "splitat" is to split group into atoms. But after I use them two, I found they are opsite. see the following example> splitres 3Splitting group 3 'MIL' into atoms> splitat 3Splitting group 3 'MIL' into residues2006/9/15, Qiao Baofu < [EMAIL PROTECTED]>:Hi AllI have 2 questions about using g_rdf -com: 1. In the manual, it is said that when -com option used, the rdf is calculated with respect to the center of first group. My question is that, if i want to calculate the rdf of the COM of two groups, how to do it? 2. In my mind, for single-atom, the COM should just be the center of it. Therefore, if I calculate the rdf of two single-atom groups WITH and WITHOUT -com option, the result should be the same. However, it is not that case. I calculated the rdf of H-Cl in these two methods, and got quite different result!! see the attachment. Why? PS: I use gromacs 3.3.1.-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)
2006/9/14, Mark Abraham <[EMAIL PROTECTED]>: Probably your interconnects between nodes are using carrier pigeons orsomething :-) I expect that 1 cpu on machine A will require around fourtimes as long as 1 4-cpu node, which you can presumably test for yourself. It is forbidden to run only one cpu on the cluster A in my inisititute. For next time, if you want to compare hardware like this, either use thesame length of time or the same number of MD steps for all of your runs.Also when reporting runtimes, make it clear whether you are reporting walltime or some time * number_of_cpus, etc. :-)For all the jobs (except the one on my local computer) , I set walltime=1hour, and nsteps= 200,000,dt=0.001.The running time are taken from the end of the .log file. See the following example. NODE (s) Real (s) (%) Time: 1581.000 1581.000 100.0 26:21 (Mnbf/s) (GFlops) (ns/day) (hour/ns)Performance: 56.376 4.515 10.930 2.196Mark___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Re: Re: Question about parallazing Gromacs
Thanks a lot!2006/9/14, Cesar Araujo <[EMAIL PROTECTED]>: > -->> Message: 7> Date: Thu, 14 Sep 2006 09:27:45 +0200> From: "Qiao Baofu" <[EMAIL PROTECTED]>> Subject: Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao > Baofu)> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>> Message-ID:> < [EMAIL PROTECTED]>> Content-Type: text/plain; charset="iso-8859-1">> Hi,>> Thanks. I have test different cpus. Our institute has two clusters: one is > each node has 4 cpu (A), one is one node has only 1 cpu (B). I made> different tests on the two clusters and my local computer using the same> system. See the following result:>> A (For 1 hour) ># of cpus ;MD steps> 4 finished (20steps for 26:21)> 8 finished (20steps for 40:57)> 12 87950> 20 42749 > 44 5962 !> B (For 1 hour)> # of cpu ; MD steps> 1156991 for 56:12> 2179820> 3200,000 for 54:20 > 4200,000 for 51:12> c. Local(single cpu), 20 steps For 1h52:38>> One can see that> 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local> computer. > 2. More than one nodes will decrease the performancs the gromacs,> 3. On cluster B, the more cpu used, the faster gromacs runs. But the> difference of speed is not apparent.> 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node (4 > cpus)>> I wonder if anyone can tell the bottlenack: the hardware on the cluster or> gromacs?>>Well, probably it is a combination of bottlenecks in both software andhardware. Both of them should be optimized to guarantee the best performance. From thehardware side the delays in inter-node communication across the network canbe the reason. But also, it can be related with software issues related to the operatingsystem and network configuration. I think that the first thing to do is workin clustersetup to achieve the best performance for your hardware configuration.In addition, take into account that inter-node communication between two CPU'sinside the same machine should be faster than between two CPU's across thenetwork.>From the software side (Gromacs) the algorithms should be optimized withregardto the parallel programming model. David said in a previous answer that they have detected some problems in the software implementation and they areworkingto solve that issue in the next version of Gromacs.Regards,--- Cesar Araujo, Lic. of ChemistryDepartment of Molecular EndocrynologyOulu University HospitalFIN-90029 OYS, OULU, FINLANDphone: +358 8 3155632e-mail: [EMAIL PROTECTED] ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies Max-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)
Hi,Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using the same system. See the following result: A (For 1 hour) # of cpus ; MD steps 4 finished (20steps for 26:21) 8 finished (20steps for 40:57) 12 87950 20 42749 44 5962 ! B (For 1 hour) # of cpu ; MD steps 1 156991 for 56:12 2 179820 3 200,000 for 54:20 4 200,000 for 51:12 c. Local(single cpu), 20 steps For 1h52:38One can see that 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local computer.2. More than one nodes will decrease the performancs the gromacs, 3. On cluster B, the more cpu used, the faster gromacs runs. But the difference of speed is not apparent.4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node (4 cpus)I wonder if anyone can tell the bottlenack: the hardware on the cluster or gromacs? 2006/9/14, Mark Abraham <[EMAIL PROTECTED]>: > You have to> find your optimum making some tests with your settings. To do that you can> start your simulation and interrupt after a while to have some data logged> in the log file. Then, from the information in that log file you can > estimate the time that the whole task will take and compare using more or> less number of processors until you find your optimum value.Of course, that "while" should be at least of the order of several minutes. There is a set-up cost borne once at the start of the calculationwhich is not proportional to the length of the calculation, so you need torun long enough to get out of the time period during which it dominates the linear component.Mark___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Sincerely yours,** Baofu Qiao, PhDFrankfurt Institute for Advanced Studies** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to write a annealing .mdp
Hi, set T_couple=no and refer to the following script; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic)annealing = single; Number of time points to use for specifying annealing in each group annealing_npoints = 6; List of times at the annealing points for each groupannealing_time = 0 10 20 30 40 50; Temp. at each annealing point, for each group.annealing_temp = 425 375 325 275 245 203 在06-9-13，zzhwise1 <[EMAIL PROTECTED]> 写道： hello everyone i want to anneal my system,but i don't konw how to wrote a right annealing-mdp! could anyone give me a moldel? tanks in advaced! 3G 时 代 来 临 了，坚 决 对 传 统 邮 箱 说 不 ！ 新 一 代 极 速 3G 邮 箱 闪 亮 登 场 ，280 兆 网 盘 免 费 送 ！ 点 击 此 处 注 册 ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about parallazing Gromacs
Hi all,I have a question about parallazing gromacs: I run the same system on a cluster of my institute and my local computer, Cluster: dual processor boards AMD Opteron 270 (Dual-Core), 2.0 GHz Local computer: AMD X86-64 Cpu, double precision1. The cluster (nodes=3:ppn=4) runs 87950 MD steps for one hour2. The cluster (nodes=5:ppn=4) runs 42749 MD steps for one hour 3. The cluster (nodes=11:ppn=4) runs 5962 MD steps for one hour 3. My local computer runs 179090 MD steps For 1hour 51 mintues.It is verry strange that the more cpus I use, the slowest the gromacs runs.!! Who knows what's wrong with my job? And for paralleled gromacs, how many cpus is prefered?The grompp command is: grompp -np 12 -o md3.mdp -c md3in.gro -p MCl.top -o md3.tprThe following is one of the the job scripts on the cluster: ## MD NTP(Berendsen&Berendsen, T=425&P=1bar),200ps tau_p=4###!/bin/bash#PBS -N "md3"##PBS -l walltime=01:00:00,nodes=3:ppn=4##PBS -m abe##PBS -o md3.out ##PBS -e md3.err##cd /work/fias/qiao/time_checking/nodes3//usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/lamboot $PBS_NODEFILE/usr/local/Cluster-Apps/lam/gcc/64/7.1.1/bin/mpirun -np 12 mdrun -v -s md3.tpr -x md3 -e md3 -c md3 -g md3exit 0 -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced Studies** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about angle constraints
Hi David,I think maybe the virtual site is suitable for NO3-. But how about PF6-? Please see the .itp file for the PF6-, which is wroten by myself.1. Because all the bond-length are constrainted, there is no energy term in the .itp file. Therefore it is not a problem of energy term, I think. 2. Except the bond-length, the angles F-P-F should be constrainted to be 90 or 180.*** .itp file*[ moleculetype ]; Name PF6- PFN 3[ atoms ]; nr type resnr resid atom cgnr charge mass 1 opls_977 1 PFN PAA 1 1.34 30.97376 2 opls_978 1 PFN FAA1 1 -0.39 18.99840 3 opls_978 1 PFN FAA2 1 -0.39 18.99840 4 opls_978 1 PFN FAA3 1 - 0.39 18.99840 5 opls_978 1 PFN FAA4 1 -0.39 18.99840 6 opls_978 1 PFN FAA5 1 -0.39 18.99840 7 opls_978 1 PFN FAA6 1 -0.39 18.99840[ constraints ] 1 2 1 0.1560 1 3 1 0.1560 1 4 1 0.1560 1 5 1 0.1560 1 6 1 0.1560 1 7 1 0.1560; The structure of PF6- is Octahedral[ constraints ] 2 3 2 0.2206 2 4 2 0.2206 2 5 2 0.3120 2 6 2 0.2206 2 7 2 0.2206 3 4 2 0.2206 3 5 2 0.2206 3 6 2 0.3120 3 7 2 0.2206 4 5 2 0.2206 4 6 2 0.2206 4 7 2 0.3120 5 6 2 0.2206 5 7 2 0.2206 6 7 2 0.2206 *** .top file** ;the force field files to be included#include "ffoplsaa.itp"; include the PF6- topology#include "PFN.itp"[ system ]PFN[ molecules ]; molecule name number PFN 52006/8/30, David van der Spoel <[EMAIL PROTECTED]>: Qiao Baofu wrote:> Hi All,>> In my simulation, the NO3- is used, in which the three N-O bond length > is constraints. And a planar triangular structure is used.> I used the type "1" of [ constraints ] to constraint the bond length.> Because I only find angle constraints which is used on H-involved angles, > I used the type "2" of [ constraints ] to constraint the length between> Os. (The distance is calculated from the triangular structure). After> the Energy Minimization, all the bong length become very long (much > bigger than the box length). Who knows how to solve it?>You probably have an error in the topology. Check energy terms.However, you probably should consider modeling this using either an improper dihedral to keep the N in the plane or, if you want to keep themolecule planar at every time use a virtual site representation for the N.> Sincerely yours,> Baofu Qiao, PhD>> > >> ___> gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the> www interface or send it to [EMAIL PROTECTED].> Can't post? Read http://www.gromacs.org/mailing_lists/users.php --David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,Baofu Qiao, PhD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about angle constraints
Hi All,In my simulation, the NO3- is used, in which the three N-O bond length is constraints. And a planar triangular structure is used. I used the type "1" of [ constraints ] to constraint the bond length. Because I only find angle constraints which is used on H-involved angles, I used the type "2" of [ constraints ] to constraint the length between Os. (The distance is calculated from the triangular structure). After the Energy Minimization, all the bong length become very long (much bigger than the box length). Who knows how to solve it? Sincerely yours,Baofu Qiao, PhD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
