[gmx-users] Phd positions available
Dear all, since many people in our group are gromacs users, this announcement could make some sense on the gmx mailing list. Please forward it to interested people. Best wishes, Giovanni Bussi ***PhD positions at SISSA in Physics and Chemistry of Biological Systems There are 3 positions available for the PhD in Physics and Chemistry of Biological Systems at the International School for Advanced Studies, Trieste, Italy. Applicants should have a good background in Physics, Chemistry or related subjects and are expected to obtain their Laurea Specialistica or equivalent degree by Autumn 2011. Applicants will be first screened based on their CV (educational track record, letters of presentation, preprints or publications). Those that pass the preliminary screening will be invited to participate to the local selection taking place on October 5 and 6. Admitted students will have the opportunity to follow a one-year educational program in an international and interdisciplinary environment, followed by two or three years of active research in one of the following areas: * structural bioinformatics, * statistical mechanics of complex molecular systems, * biomolecular simulations, * simulations of rare events. For further information about the available research lines, and past entrance exams see the Statistical and Biological Physics Sector website. To apply: The application should be filled exclusively online at the following address: www.sissa.it/applications/phd . The application deadline is September 19th. The complete official announcement can be download here. Notice that SISSA can cover, in full or in part, the expenses of students who are admitted to the local entrance exam. Please contact p...@sissa.it for further information. About SISSA: The International School for Advanced Studies of Trieste. SISSA was the first Italian university to offer the PhD degree, and has continued to do so with notable success. Since its founding in 1978, SISSA has prepared more than 500 young people for careers in research and teaching. According to a recent independent comprehensive academic survey SISSA is one of the leading Italian research institutes in terms of density of top scientists. In the latest evaluation of the Italian university system (CIVR) it was judged as the most exciting of the small research centers in Italy in physics and mathematics and came second in biology. Facilities: People who study at SISSA, which is situated in the campus in Via Bonomea in a park of over 100,000 m2, have access to an excellent library which is open 24 hours a day; they have a computer at their disposal with which to connect to the huge resources for scientific computing and internet services; they receive support in finding accommodation in the city from the housing service and a monthly contribution from the School towards the rent; on the campus they can find a restaurant, kindergarten, and meditation and music rooms. Students from non-European Union countries have their enrollment in the Italian national health service reimbursed. Female students receive a contribution during their maternity leave. Students are awarded scholarships for the entire duration of their training programmes. ***Start Date November 2011 ***Duration 3 to 4 years ***Funding Source Italian Ministry of University ***Salary on grant Ministerial PhD fellowship integrated by SISSA for a monthly amount of ~ 100 Euros. In addition there are SISSA contributions towards house rent and purchase of personal laptop. ***Contact person Cristian Micheletti ***email miche...@sissa.it ***Group web page: www.sissa.it/sbp -- 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] Phd positions in SISSA
Dear all, since many people in our group are gromacs users, this announcement could make some sense on the gmx mailing list. Please forward it to interested people. Best wishes, Giovanni Bussi # Job Description: Applicants should have a good background in Physics, Chemistry or related subjects and are expected to obtain their Laurea Specialistica or equivalent degree by Autumn 2011. Applicants will be first screened based on their CV (educational track record, letters of presentation, preprints or publications). Those that pass the preliminary screening will be invited to participate to the local selection taking place around mid April 2011. Admitted students will have the opportunity to follow a one-year educational program in an international and interdisciplinary environment, followed by two or three years of active research in one of the following areas: * structural bioinformatics, * statistical mechanics of complex molecular systems, * biomolecular simulations, * simulations of rare events. For further information about the available research lines, and past entrance exams see the Statistical and Biological Physics Sector website (www.sissa.it/sbp) To apply: The application should be filled exclusively online at the following address: www.sissa.it/applications/phd . The application deadline is March 31st. Notice that SISSA can cover, in full or in part, the expenses of students who are admitted to the local entrance exam. Please contact p...@sissa.it for further information. About SISSA: The International School for Advanced Studies of Trieste. SISSA was the first Italian university to offer the PhD degree, and has continued to do so with notable success. Since its founding in 1978, SISSA has prepared more than 500 young people for careers in research and teaching. According to a recent independent comprehensive academic survey SISSA is the leading Italian university in terms of density of top scientists. In the latest evaluation of the Italian university system (CIVR) it was judged as the most exciting of the small research centers in Italy in physics and mathematics and came second in biology. Facilities: People who study at SISSA, which is situated in the campus in Via Bonomea in a park of over 100,000 m2, have access to an excellent library which is open 24 hours a day; they have a computer at their disposal with which to connect to the huge resources for scientific computing and internet services; they receive support in finding accommodation in the city from the housing service and a monthly contribution from the School towards the rent; on the campus they can find a restaurant, kindergarten, and meditation and music rooms. Students from non-European Union countries have their enrolment in the Italian national health service reimbursed. Female students receive a contribution during their maternity leave. Students are awarded scholarships for the entire duration of their training programmes. Start date: November 2011. Earlier starts are possible through pre-doctoral scholarships. Duration: 3 to 5 years Funding Source: MIUR Salary on grant: SISSA tops the Ministerial doctoral salaries with an additional financial contribution and provides benefits such as partial support of house rent, laptop equipment etc. Please contact p...@sissa.it to enquire about the current exact amount of the various financial aspects Contact Person (Referent): Cristian Micheletti Ref. E-Mail: miche...@sissa.it Group Web Page: http://www.sissa.it/sbp -- 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] Phd positions
Dear all, since many people in our institute are gromacs users, this announcement could make some sense on the gmx mailing list. Please forward it to interested people. Best wishes, Giovanni Bussi # Dear colleague, we would like to remind the forthcoming deadline - September 23 - for the application for the "PHD IN PHYSICS AND CHEMISTRY OF BIOLOGICAL SYSTEMS" at SISSA, Trieste. This year we have 5 positions available, for Italian and foreigner students. The application should be filled exclusively online at the following address: www.sissa.it/applications/phd For further information about the available research lines, see the website http://www.sissa.it/sbp Notice that SISSA can partially cover the travel expense for students willing to participate to the entrance exam. Please forward this information to interested students and colleague. Best wishes, on behalf of the PhD faculty, C. Micheletti, A. Laio and G. Bussi -- 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] PLUMED tutorial announcement
Dear all, We are proud to announce a CECAM tutorial on PLUMED. PLUMED is an open source plugin for free-energy calculations in molecular systems that can be interfaced, through a simple patch procedure, with some of the most popular classical molecular dynamics codes, including AMBER, GROMACS, NAMD and DLPOLY. With PLUMED, the user can perform several types of calculation, including metadynamics, umbrella sampling and steered molecular dynamics. More information on PLUMED can be found at http://merlino.mi.infn.it/~plumed The tutorial will be held in Lausanne, Switzerland, September 28, 2010 to October 1, 2010. The list of lecturers will include Davide Branduardi, Giovanni Bussi, Fabio Pietrucci, Massimiliano Bonomi, Francesco Luigi Gervasio, Alessandro Laio, and Michele Parrinello. Strict deadline for application is May 31 CECAM will cover hotel/meal expenses for all the participants. Since the number of available places is limited, applicants will be selected on the basis of their curriculum and scientific interests. Acceptance for participation will be communicated within June 15. More information on the tutorial can be found at: http://www.cecam.org/workshop-407.html http://sites.google.com/site/plumedtutorial2010 The Organizers, Davide Branduardi, Giovanni Bussi and Fabio Pietrucci -- 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] free energy perturbation
I will try the second solution you proposed (which seems more flexible). So, I should edit the top file (as explained in the "Topologies/File formats/Topologies for free energy calculations" section of the manual). And I should NOT use "couple-moltype" anymore, which is just a shortcut for the standard case of switching a single molecule. Right? Thanks a lot Berk. Giovanni On Mon, Dec 14, 2009 at 3:49 PM, Berk Hess wrote: > > >> From: giovanni.bu...@gmail.com >> Date: Mon, 14 Dec 2009 13:47:37 +0100 >> To: gmx-users@gromacs.org >> Subject: [gmx-users] free energy perturbation >> >> Dear all, >> >> I am using GROMACS with free-energy perturbation to switch off a >> molecule gradually. If I understand correctly, the parameter >> "couple-moltype" is used to select which molecule to switch off. Is it >> possible to switch off *two* molecules at the same time? (e.g. a >> charged molecule and a neutralizing ion). > > I have not implemented this yet. > It would indeed be useful. > >> >> In case not, is there any problem related to the fact that in one of >> the topologies the total charge is not zero? > > Yes, this will create problems, because you are then also calculating the > cost > of building up a uniform backbground charge, both in case of PME and RF. > > Note that free-energies of solvation of ions are huge numbers and are > relatively > difficult to determine, both in simulation and in experiment. > > There are two way to work around this problem: > Put both molecules together in one moleculetype definition. > Or simply manually set the LJ and charge of the ion to zero in the A or B > state topology. > > Berk > >> >> Thanks a lot, >> >> Giovanni >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 > > > New Windows 7: Simplify what you do everyday. Find the right PC for you. > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] free energy perturbation
Dear all, I am using GROMACS with free-energy perturbation to switch off a molecule gradually. If I understand correctly, the parameter "couple-moltype" is used to select which molecule to switch off. Is it possible to switch off *two* molecules at the same time? (e.g. a charged molecule and a neutralizing ion). In case not, is there any problem related to the fact that in one of the topologies the total charge is not zero? Thanks a lot, Giovanni -- 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] Install gromacs333 with plumed110
This question is more appropriate to the plumed-users forum. Giovanni On Thu, Aug 6, 2009 at 4:42 PM, osmair oliveira wrote: > Hi, > I am trying to install gromacs 3.3.3 with plumed 1.1.0 with the following > commands: > $ export plumedir=/home/osmair/programs/PLUMED-1.1.0 > $ CC=gcc CXX=g++ ./configure --enable-double --program-suffix=_plumed > --enable-fortran --enable-mpi > CPPFLAGS=-I/home/osmair/programs/fftw-3.0.1/include > LDFLAGS=-L/home/osmair/programs/fftw-3.0.1/lib > LD_LIBRARY_PATH=/home/osmair/programs/openmpi-1.2.7/lib > $ ./plumedpatch_gromacs_3.3.3.sh -patch > $make > > However I found the error: > /usr/lib/gcc/x86_64-redhat-linux/3.4.6/libfrtbegin.a(frtbegin.o): In > function `main': > (.text+0x1e): undefined reference to `MAIN__' > collect2: ld returned 1 exit status > make[3]: *** [ffscan] Error 1 > make[3]: Leaving directory > `/home/osmair/programs/gromacs-333PLUMED/src/kernel' > make[2]: *** [all-recursive] Error 1 > ... > > On the other hand, when I try install the gromacs without plumed, the > following commands work very well. > $ CC=gcc CXX=g++ ./configure --enable-double --program-suffix=_plumed > --enable-fortran --enable-mpi > CPPFLAGS=-I/home/osmair/programs/fftw-3.0.1/include > LDFLAGS=-L/home/osmair/programs/fftw-3.0.1/lib > LD_LIBRARY_PATH=/home/osmair/programs/openmpi-1.2.7/lib > $ make > > Someone can help me? > > Thanks > > Ph.D. Osmair Vital de Oliveira > Federal University of Sao Carlos - Brazil > > > Quer uma internet mais segura? Baixe agora o novo Internet Explorer 8. É > grátis! > ___ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
Dear Xavier, With the default flag for pbc (periodic_molecules=no) you may end up in lincs problem if an atom of the protein becomes too close to the image of another atom of the protein. If this is your case, use periodic_molecules=yes, or enlarge the solvation cell. Hope this helps, Giovanni On Wed, Jun 3, 2009 at 10:48 AM, Erik Marklund wrote: > XAvier Periole skrev: >> >> On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote: >> >>> Hi XAvier, >>> Do you use virtual sites? I've seen this when I used virtual sites, >> >> No virtual sites. >>> >>> large time steps and a system that probably wasn't equilibrated enough. >> >> time step 2 fs and a system totally equilibrated, nothing there. >> >> I would have considered this if the warning were reproduced when >> restarting the simulation. >> >> It seems more that it is a loss of accuracy due to communication >> between CPUs ? >> > If you use dynamic load balancing then you are sacrificing binary > reproducibility. Because of this, and the chaotic nature of MD, the error > will likely not occur at the same point in your continuation. Still, the > source of the error persists and is what demands attention I'd say. >> >> XAvier. >> >>> Ran. >>> >>> XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding "-cpi md.cpt" to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ gmx-users mailing list gmx-us...@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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> ___ >>> gmx-users mailing list gmx-us...@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 mailing list gmx-us...@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 thewww interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > --- > Erik Marklund, PhD student > Laboratory of Molecular Biophysics, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys > > ___ > gmx-users mailing list gmx-us...@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 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] Re: v-rescale - harmonic oscillator
Dear Servaas,
the problem that you found is not related to the stochastic rescaling
itself, but to the way the effective energy is calculated in gromacs.
In particular, the increment in the integral part is not consistent
with the applied scaling. You can correct for this by changing
src/mdlib/coupling.c, line 462:
// NEW:
if (Ek + dEk <= 0) {
ekind->tcstat[i].lambda = 0.0;
therm_integral[i] -= -Ek;
} else {
ekind->tcstat[i].lambda = sqrt((Ek + dEk)/Ek);
ekind->tcstat[i].lambda = max(min(1.25,ekind->tcstat[i].lambda),0.8);
therm_integral[i] -=
Ek*(ekind->tcstat[i].lambda*ekind->tcstat[i].lambda-1.0);
}
// OLD:
// if (Ek + dEk <= 0) {
// ekind->tcstat[i].lambda = 0.0;
// } else {
// ekind->tcstat[i].lambda = sqrt((Ek + dEk)/Ek);
// ekind->tcstat[i].lambda = max(min(1.25,ekind->tcstat[i].lambda),0.8);
// }
// therm_integral[i] -= dEk;
Note that this is a problem only when lambda is very different from
one, and this happens in very small systems. The effect for large
systems should be negligible. Furthermore, you should combine this
with the fix that Berk posted a few days ago, which is in file
src/mdlid/update.c, line 165:
// OLD:
// vv = lg*(vn + f[n][d]*w_dt);
// NEW:
vv = lg*vn + f[n][d]*w_dt;
These fixes will give you a much better energy conservation.
Consider also the following comments:
* For very small systems, the special cases for lambda (max(min...))
introduce small artifacts in the ensemble which are out of control.
Thus, I don't think that you can really use this scheme to perform
rigorous hybrid Monte Carlo. A possible solution is to use a better
integrator for the thermostat (the one discussed in the appendix of
Bussi, Donadio and Parrinello, JCP 2007), which works for every choice
of taut and any number of degrees of freedom, thus it does not need
any special case for lambda. I can send you an implementation of it
for gromacs. Berk is also working on that, and will probabily
introduce it soon in the official gromacs (4.1 or the cvs).
* Even with all these fixes (including the better integrator), there
still a (small) drift in the effective energy for the harmonic
oscillator. I did not test, but I guess that it originates from the
fact that gromacs uses leapfrog and not velocity-Verlet, and leapfrog
is not easily combined with our stochastic scheme which is ultimately
based on Trotter decomposition. The drift should *completely*
disappear for a harmonic system integrated with velocity-Verlet. If
you are interested, we have proven this for a different thermostat
(Bussi Parrinello, PRE 2007, for Langevin dynamics). The demonstration
can be straightforwardly ported to the velocity-rescaling thermostat.
* A part from the two previous implementation issues, I do not expect
any problem with the stochastic rescaling applied to the harmonic
oscillator. In particular, lack of ergodicity in harmonic systems
(which is the big pain in Nose-Hoover) should not be a problem at all.
Furthermore, the algorithm should work and provide the proper ensemble
also on very small systems.
Best regards,
Giovanni Bussi
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