Re: [gmx-users] updated OPLS/AA
Alan skrev: Can someone confirm that GMX 4.x is already released with updated OPLS/AA files as once mentioned in http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,7/Itemid,26/ ? Yes. It has been possible to use OPLS-AA in GROMACS for a long time. Kind regards Andreas ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Charges in SW water model
Dear Professor Spoel. I have a question concerning your article on the SW water model published in J. Phys. Chem. B, 105, 2618-2626 (2001). I guess the question is only indirectly related to GROMACS, but I'll post in on the mailing list since it may be of interest to other GROMACS users as well. Equation (4) of the paper states that k_nn = (q_s)^2/alpha_nn, where nn is either xx, yy or zz. k is the spring constant, q_s is the charge and alpha is the polarizability. The first line in section 2.2 of the paper is "After determining the charges and spring constants corresponding to the polarizabilities...". It seems as if the are too many unknowns in the equation above, or do I miss something? If I understand it correctly, the spring constants are determined from q_s and alpha. But how is the charge determined? Hope you can help with this question. Kind regards Andreas -- ###### Andreas Kring, Ph.D.-student University of Copenhagen Niels Bohr Institute Universitetsparken 5 DK-2100 Copenhagen Denmark Phone Office (D304): (+45) 35 32 04 91 Home: (+45) 77 42 55 78 Mobile:(+45) 61 77 55 78 E-mail: [EMAIL PROTECTED] ___ 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] MD run, polarizable molecules, EM did not converge
Hello all. I've been searching the archives with no luck so here goes: I am using shell molecular dynamics to simulate a hydroxide ion dissolved in water. I have been using the steepest descent minimizer (tried in the range from 30 to 70 steps) to minimize the system, but I'm not capable of getting Fmax lower than Potential Energy = -2.39282728357508e+04 Maximum force = 2.22634509434073e+03 on atom 3 Norm of force = 5.74522076456533e+01 Running the shell MD simulation with the output from the above minimization generates a lot of "EM did not converge" (see below). As recommended in the GROMACS manual, I'm using the follow parameters in the mdp-file: emtol = 1 niter = 20 fcstep = 0 step 1: EM did not converge in 20 iterations, RMS force 307.457 step 2: EM did not converge in 20 iterations, RMS force 306.841 step 3: EM did not converge in 20 iterations, RMS force 308.809 ... Any ideas on how I can fix this? Regards Andreas ___ 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] About the gromacs 4.0 manual and parallel running
2. How to run a parallel simulation with Gromacs 4.0? Are there any special tips for a optimized parallel run? I've tried a set of runnings but found the accelerations are not good enough as I expected. I do something like this (for 8 CPUs): $ grompp -c system.gro -p topology.top -f something.mdp $ mpirun -np 8 mdrun Regards Andreas ___ 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] Gromacs-4.0: 4 CPUs crashes, works on 1 CPU
Berk Hess skrev: Hi, Could you file a bugzilla report and attach the tpr file? Please also mention at what step you get this error (run mdrun -v to get the step numbers). Berk Sure, no problem. Regards Andreas ___ 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] Gromacs-4.0: 4 CPUs crashes, works on 1 CPU
Andreas Kring skrev: Hi all. I have just installed GROMACS 4.0. My system consists of one hydroxide ion and 999 polarizable water molecules. When the system is minimized (using only one CPU) with a steepest descent minimizer, there are no problems. But when I try to minimize exactly the same system using 4 or 8 CPUs, I get the following error: Sorry... forgot to write which commands I used: $ grompp_d -c system.gro -p topol.top -f steep.mdp followed by $ mpirun -np 4 mdrun_d I have no problems running in parallel in version 3.3.3. Regards Andreas ___ 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] Gromacs-4.0: 4 CPUs crashes, works on 1 CPU
Hi all. I have just installed GROMACS 4.0. My system consists of one hydroxide ion and 999 polarizable water molecules. When the system is minimized (using only one CPU) with a steepest descent minimizer, there are no problems. But when I try to minimize exactly the same system using 4 or 8 CPUs, I get the following error: Reading file topol.tpr, VERSION 4.0 (double precision) Making 1D domain decomposition 4 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 10 A list of missing interactions: exclusions of 14987 missing -1 --- Program mdrun4_d, VERSION 4.0 Source code file: domdec_top.c, line: 337 Software inconsistency error: One or more interactions were multiple assigned in the domain decompostion --- "Microsecond Here I Come" (P.J. Van Maaren) Error on node 0, will try to stop all the nodes Halting parallel program mdrun4_d on CPU 0 out of 4 gcq#161: "Microsecond Here I Come" (P.J. Van Maaren) Any ideas why this could be? Regards Andreas ___ 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] question about default parameter for g_hbond
Thomas Schlesier skrev: Hi all, does somebody know from where the default parameters for g_hbond (angle Acceptor-Hydrogen-Donor = 30° ; distance Acceptor-Donor = 0.35nm) are? I found nothing in the manual about that. Maybe you can find a hint in Luzar et al., J. Chem. Phys., 98, 8160 (1993) Regards Andreas ___ 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] Charge groups, PME and ions [SOLVED]
David van der Spoel wrote: Andreas Kring wrote: Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent). For this molecule it is not possible to make charge groups with a total charge of zero (or and integer number). Is this best solved by using a separate charge group for each atom?... and is this allowed since the charge of such a charge group is not zero? According to the manual, the charge groups are used to make neighbor lists... but these are only important with respect to the computational speed as long as PME is used to deal with electrostatic interactions? Or have I misunderstood this? For such a small molecule you can have separate charge groups for each atom when using PME. Efficiency gains will be minimal when grouping atoms into charge groups. Great! Thanks a lot. /Andreas ___ 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] Charge groups, PME and ions
Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent). For this molecule it is not possible to make charge groups with a total charge of zero (or and integer number). Is this best solved by using a separate charge group for each atom?... and is this allowed since the charge of such a charge group is not zero? According to the manual, the charge groups are used to make neighbor lists... but these are only important with respect to the computational speed as long as PME is used to deal with electrostatic interactions? Or have I misunderstood this? /Andreas ___ 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] Bonds missing in VMD visualization [SOLVED]
Thank you for solution suggestions! Solution 1 worked out just fine. After a little Goolgeing it seemed as if solution 2 requires modification of the VMD source code. Solution 3 also looks attractive - I'll have a closer look at this later on... /Andreas Diego Enry skrev: So I was testing on VMD the C-CL bond distance to draw a bond. Actually, the limit was a disturbing 1.80A ! So close to the 1.81A you need :( Solutions ! 1) Use "dynamic bonds representation" and set the cut-off to 1.81 or more 2) Find where VMD sets it's standard cutoff for bonds and set it to 1.81 or more forever. 3) VMD FAQ solution is to make a .PSF (topology) to solve this problem. ( You will only need the bond list ) http://www.ks.uiuc.edu/Research/vmd/allversions/vmd_faq.html How to write a .PSF file http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html On Tue, Sep 2, 2008 at 5:59 AM, Andreas Kring <[EMAIL PROTECTED]> wrote: Thank you for your reply. I tried the following: VMD computes distances between pairs of atoms to "draw" a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL should be around 1.76A. In 1,1,1-trichloroethane the C-Cl bond distance should be around 1.81A. I checked the C-Cl bond distances using g_bond and this give a nice Gaussian distribution around 1.81A (which matches what is in the topology file). VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb you open before the .xtc/.trr), this distance is greater than 2.0A. All bond distances are less than 2.0A, but VMD still does not draw a bond? Is there anything else I can try? /Andreas ___ 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 -- ###### Andreas Kring, Ph.D.-student University of Copenhagen Niels Bohr Institute Universitetsparken 5 DK-2100 Copenhagen Denmark Phone Office (D304): (+45) 35 32 04 91 Home: (+45) 77 42 55 78 Mobile:(+45) 61 77 55 78 E-mail: [EMAIL PROTECTED] ___ 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] Bonds missing in VMD visualization
Thank you for your reply. I tried the following: VMD computes distances between pairs of atoms to "draw" a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL should be around 1.76A. In 1,1,1-trichloroethane the C-Cl bond distance should be around 1.81A. I checked the C-Cl bond distances using g_bond and this give a nice Gaussian distribution around 1.81A (which matches what is in the topology file). VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb you open before the .xtc/.trr), this distance is greater than 2.0A. All bond distances are less than 2.0A, but VMD still does not draw a bond? Is there anything else I can try? /Andreas ___ 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] Bonds missing in VMD visualization
Hello, I have run an MD simulation of 1000 1,1,1-trichloroethane molecules and it all worked nicely. But when I try to visualize the trajectory file in VMD some of the C-Cl bonds are missing (although all the atoms appear on the screen - only bonds are missing)? Can I do anything to fix this? /Andreas ___ 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] Save all MD snapshot
Collins Nganou skrev: Dear Users. Greetings. Please someone can tell me how can I proceed to save all MD snapshot for a long time simulation after equilibration. You can set the parameters below to the value "1" in the configuration file for mdrun. nstxout = 1 nstvout = 1 nstfout = 1 /Andreas ___ 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] Arguments to g_rdf [SOLVED]
Exactly what I was looking for! Thanks a lot! /Andreas Justin Lemkul skrev: Is this what you are looking for? http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive -Justin Andreas Kring wrote: Hello all, Is it somehow possible to pass arguments to g_rdf from the command line or a file, such that g_rdf will not prompt me for which groups I want to calculate the rdf for? For example, I have an .ndx file for water containing the groups [SYSTEM] [SOL] [OW] [HW1_HW2] and I would like to calculate the oxygen-hydrogen RDF without being prompted by g_rdf? (the reason is that I have a small Python script running the calculations for me, which could make use of this). Best regards Andreas ___ 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 -- ###### Andreas Kring, Ph.D.-student University of Copenhagen Niels Bohr Institute Universitetsparken 5 DK-2100 Copenhagen Denmark Phone Office (D304): (+45) 35 32 04 91 Home: (+45) 77 42 55 78 Mobile:(+45) 61 77 55 78 E-mail: [EMAIL PROTECTED] ___ 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] Arguments to g_rdf
Hello all, Is it somehow possible to pass arguments to g_rdf from the command line or a file, such that g_rdf will not prompt me for which groups I want to calculate the rdf for? For example, I have an .ndx file for water containing the groups [SYSTEM] [SOL] [OW] [HW1_HW2] and I would like to calculate the oxygen-hydrogen RDF without being prompted by g_rdf? (the reason is that I have a small Python script running the calculations for me, which could make use of this). Best regards Andreas ___ 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] grompp error, invalid line in .gro file [SOLVED]
Your formatting is incorrect. The .gro format is a very old GROMOS fixed format (not free format). See the manual for the details: http://www.gromacs.org/documentation/reference/online/gro.html Thanks a lot. Now everything works perfectly! /Andreas ___ 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] grompp error, invalid line in .gro file
Justin A. Lemkul skrev: Just thinking out loud, but maybe "Argon" is too long of a name for the residues. The longest I think I've seen is 4 characters (something like LYSH or ARGN, for example). Maybe the length of the name is throwing off the formatting. Why don't you try again with a residue name of something like AR (in both the .top and .gro, of course) and see if that fixes things. It doesn't seem to work... I've tried the topology file below (with a similar change in the .gro file)... Kind regards Andreas ; Topology file for Ar ; Parameter level #include "ffoplsaa.itp" ;#define _FF_OPLS ;#define _FF_OPLSAA ;[defaults] ;#include "ffoplsaanb.itp" ; [atomtypes] ;#include "ffoplsaabon.itp" ; [bondtypes] ; [constrainttypes] ; [angletypes] ; [dihedraltypes] ; Molecule level [ moleculetype ] ; molname nrexcl Arg 1 [ atoms ] ; idat_type res_nr res_nameat_name cg_nr charge 1 opls_0971 Arg Ar 1 0.0 ; System level [ system ] Argon liquid [ molecules ] Arg 2048 ___ 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] grompp error, invalid line in .gro file
Hello all. I'm trying to simulate an argon liquid. The OPLS-AA force field is used with the files from /usr/local/gromacs/share/gromacs/top. But I get an error when I run $ grompp -f NVT.mdp -c Ar.gro -p Ar.top --- Program grompp, VERSION 3.3.3 Source code file: confio.c, line: 709 Fatal error: Invalid line in Ar.gro for atom 1: 1Argon Ar 1 0.0 0.0 0.0 --- An ideas on what can be wrong? My argon .top file and .gro file can be seen below. Kind regards Andreas -- Ar.top -- ; Topology file for Ar ; Parameter level #include "ffoplsaa.itp" ;#define _FF_OPLS ;#define _FF_OPLSAA ;[defaults] ;#include "ffoplsaanb.itp" ; [atomtypes] ;#include "ffoplsaabon.itp" ; [bondtypes] ; [constrainttypes] ; [angletypes] ; [dihedraltypes] ; Molecule level [ moleculetype ] ; molname nrexcl Argon 1 [ atoms ] ; idat_type res_nr res_nameat_name cg_nr charge 1 opls_0971 Argon Ar 1 0.0 ; System level [ system ] Argon liquid [ molecules ] Argon 2048 - Ar.gro - fcc lattice of argon atoms 2048 1Argon Ar 1 0.0 0.0 0.0 2Argon Ar 2 0.283835 0.283835 0.0 ... 2047Argon Ar 2047 4.257525 3.97369 4.257525 2048Argon Ar 2048 3.97369 4.257525 4.257525 4.54136 4.54136 4.54136 ___ 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] Re: Wrong heat capacity (water)
Continuation of thread http://www.gromacs.org/index.php?option=com_wrapper&Itemid=84 (answered by David van der Spoel) >> Hello all, >> >> I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules, >> density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This >> works out fine, i.e. I get a correct radial distribution function >> (g_OO), but the heat capacity (C_V) is wrong. I calculated it using the >> command: >> >> $ g_energy -f ener.edr -ndf 6 -nmol 976 >> >> and get the value below (which sould have been approximately 75 J/(mol*K)). >> >> Is the command above incorrect?' >Not necessarily. It would be good if you check the following things: > >- is the simulation in equilibrium? >- how large are the fluctuations for the equilibrium part? >- is the density correct? > >You can compute the cV from the fluctuations manually as well. Does that >match the value computed by the program? > Thanks for you answer. Yes, you were right. The simulation was not in equilibrium. I've run a new simulation which I have made sure is in equilibrium. I have also checked that the density is correct, as you suggest above, using the g_density command. The numbers for the new simulation can be seen below (same simulation conditions as stated in the top of this mail), and the answer is still not right? With the command $ g_energy -f ener.edr -ndf 6 -nmol 976 I get Cv = 305.413 J/(mol*K), while a manual calculation gives Cv = 1/(k_B*T*T)*Var(E) = 85.6 J/(mol*K), where Var(E) was found using the RMSD numbers remembering that the unit of these are kJ/mole. The table value is Cv equal to approximately 75 J/(mole*K). Any ideas? Kind regards Andreas Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -41.3012 0.219318 08.76027 87.6114 Kinetic En. 7.48311 0.135439 04.46649 44.6693 Total Energy -33.8181 0.256267 013.2266 132.28 Temperature 300.0025.429825.40392 0.183467 1.83485 Pressure (bar) -269.723384.283384.1333.71038 37.1075 Heat Capacity Cv: 305.413 J/mol K (factor = 0.639443) ___ 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] Wrong heat capacity (water)
Hello all, I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules, density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This works out fine, i.e. I get a correct radial distribution function (g_OO), but the heat capacity (C_V) is wrong. I calculated it using the command: $ g_energy -f ener.edr -ndf 6 -nmol 976 and get the value below (which sould have been approximately 75 J/(mol*K)). Is the command above incorrect? Kind regards Andreas Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -41.1524 0.478018 0 -3.69759 -36.9796 Kinetic En. 7.48322 0.282052 0 -4.33977 -43.4021 Total Energy -33.6692 0.604335 0 -8.03739 -80.3819 Temperature 300.00611.307611.2959 -0.178262 -1.7828 Heat Capacity Cv: -3.94726 J/mol K (factor = 2.77307) ___ 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] atomtypes, parameters in file do not match parameters in manual
Hello all. I'm new to Gromacs, so sorry for this (probably naive) question: In Table 5.3 in the Gromacs manual version 3.3, the parameters for [atomtypes] are: atom type, mass, charge, particle type, V and W. In the Gromacs directory containing the the force fields (/usr/local/gromacs/share/gromacs/top on my machine) the ffoplsaanb.itp file begins with the following lines: [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG Why do the manual parameters not match the parameters in the file? Which of the two are correct? Kind regards Andreas ___ 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] configure error (lam-mpi installation)
Hi all. I have tried to search the mailing archives and the FAQ, but I could not find an answer, so here goes... I'm using Ubuntu 7.10 and the latest gcc compiler in this distro is gcc-4.1.2. Being aware of the warning that the gcc-4.1.x compilers are broken, I installed gcc-4.3.0 using the usual configure; make; make install procedure. Hence, the 4.3.0 compiler is now installed in /usr/local. But when I try to install lam-mpi, I get the following error when running the configure script (with the command below) from the top lam-mpi source directory: $./configure CC=/usr/local/bin/gcc CPP=/usr/local/bin/cpp CXX=/usr/local/bin/g++ CXXLDFLAGS="-L/usr/local/lib" LDFLAGS="-L/usr/local/lib" CPPFLAGS="-I/usr/local/include" CXXCPP="-I/usr/local/include" gives *** C++ Compiler and preprocessor checking whether we are using the GNU C++ compiler... yes checking whether /usr/local/bin/g++ accepts -g... yes checking dependency style of /usr/local/bin/g++... gcc3 checking how to run the C++ preprocessor... -I/usr/local/include configure: error: C++ preprocessor "-I/usr/local/include" fails sanity check See `config.log' for more details. What am I doing wrong? (config.log file can be seen below for more details) Kind regards Andreas - config.log -- This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by configure, which was generated by GNU Autoconf 2.59. Invocation command line was $ ./configure CC=/usr/local/bin/gcc CPP=/usr/local/bin/cpp CXX=/usr/local/bin/g++ CXXLDFLAGS=-L/usr/local/lib LDFLAGS=-L/usr/local/lib CPPFLAGS=-I/usr/local/include CXXCPP=-I/usr/local/include ## - ## ## Platform. ## ## - ## hostname = yoda uname -m = x86_64 uname -r = 2.6.22-14-server uname -s = Linux uname -v = #1 SMP Tue Feb 12 03:10:53 UTC 2008 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/local/sbin PATH: /usr/local/bin PATH: /usr/sbin PATH: /usr/bin PATH: /sbin PATH: /bin PATH: /usr/games ## --- ## ## Core tests. ## ## --- ## configure:1717: checking for a BSD-compatible install configure:1772: result: /usr/bin/install -c configure:1783: checking whether build environment is sane configure:1826: result: yes configure:1877: checking for gawk configure:1906: result: no configure:1877: checking for mawk configure:1893: found /usr/bin/mawk configure:1903: result: mawk configure:1913: checking whether make sets $(MAKE) configure:1933: result: yes configure:2122: checking build system type configure:2140: result: x86_64-unknown-linux-gnu configure:2168: checking host system type configure:2182: result: x86_64-unknown-linux-gnu configure:2204: checking for lamclean configure:2237: result: no configure:2682: checking if want debugging output support configure:2696: result: no configure:2757: checking for gcc configure:2783: result: /usr/local/bin/gcc configure:3027: checking for C compiler version configure:3030: /usr/local/bin/gcc --version &5 gcc (GCC) 4.3.0 Copyright (C) 2008 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:3033: $? = 0 configure:3035: /usr/local/bin/gcc -v &5 Using built-in specs. Target: x86_64-unknown-linux-gnu Configured with: ../gcc-4.3.0/configure Thread model: posix gcc version 4.3.0 (GCC) configure:3038: $? = 0 configure:3040: /usr/local/bin/gcc -V &5 gcc: '-V' option must have argument configure:3043: $? = 1 configure:3066: checking for C compiler default output file name configure:3069: /usr/local/bin/gcc -I/usr/local/include -L/usr/local/lib conftest.c >&5 configure:3072: $? = 0 configure:3118: result: a.out configure:3123: checking whether the C compiler works configure:3129: ./a.out configure:3132: $? = 0 configure:3149: result: yes configure:3156: checking whether we are cross compiling configure:3158: result: no configure:3161: checking for suffix of executables configure:3163: /usr/local/bin/gcc -o conftest -I/usr/local/include -L/usr/local/lib conftest.c >&5 configure:3166: $? = 0 configure:3191: result: configure:3197: checking for suffix of object files configure:3218: /usr/local/bin/gcc -c -I/usr/local/include conftest.c >&5 configure:3221: $? = 0 configure:3243: result: o configure:3247: checking whether we are using the GNU C compiler configure:3271: /usr/local/bin/gcc -c -I/usr/local/include conftest.c >&5 configure:3277: $? = 0 configure:3281: test -z || test ! -s conftest.err configure:3284: $? = 0 configure:3287: test -s conftest.o configure:3290: $? = 0 configure:3303: result: yes configure:3309: checking w
