[gmx-users] PME-user for electrostatics
hi, i want to use a different function than the Coulomb to calculate the electrostatics between charged ions. So i am thinking to user the PME-user option for the electrostatics. The manual says for the PME-user optionThe PME mesh contribution is subtracted from the user table by mdrun. what that means? should i have to add the short-range-potential (given by equation-4.33 in the manual) in the user table, because that will be subtracted with the mdrun? please let me know, and thanks a lot for your help ___ 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] nematic phase disappears with reducing the time step
hi, i am doing simulations NVT simulations of rigid charged rods (with constrained bonds and stiff bending potential)in vacuum using PME for the electrostatics with a time step of 0.0015 ps (which i think is a pretty reasonable value for a corse grain model) A nematic phase of the rods appears at specific concentration (i have checked the Total-energy, Pressure, Temperature of the system and it is seems the simulation is in equilibrium) however when i do simulation of the same system with smaller time steps such as 1.0 fs or 0.5 fs, the nematic phase disappears (there is only a small increase of the potential energy comparative to that of the nematic) what is the reason that the time step can cause such an artifact phase? ___ 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] one component plasma simulations (OCP)
hi, is it possible to do one component plasma (OCP) simulations using gromacs? in the one component plasma (OCP) charged particles immersed into a homogeneous neutralizing backround. so i would guess that the neutralizing backround is the difficult thing for gromacs i would appreciate very much if you have any idea of how to do this in gromacs thanks very much ___ 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] OCP simulations
hi David A one-component plasma (OCP) is a system in which a single species of charged particle moves in a uniform backround of the opposite charge. Systems of this nature exist in the dense stellar matter of white-dwarf stars. when the screening parameter of the screened Coulomb goes to zero then we have the Coulombic one-component plasma you are right , in gromacs 3.3.1 , it is possible to use a uniform neutralizing backround in PME to compensate for a system with a net backround charge. it is not necessary to add counterions to neutralize the system. thank you very much ___ 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] RDF values lower than 1
Hi, i calculate the RDF from NVT simulation of a solution of polyelectrolyte chains and their counterions. The RDF calculated is between the monomers of the chains and the counterions. I would expect that the equilibrated value of RDF would be 1. However it is always lower than 1, at values of 0.9-0.95. Whats the reason of that , is anything wrong with my simulation? I do a long enough run to stabilize the total energy of the system and temperature Thanks in advance for your help Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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] stochastic dynamics and barostat in Gromacs
Hi all, I want to simulate a polyelectrolyte chain with its counterions in solution in NPT ensemble. it is well known that for such a system stochastic dynamics is usually used (Langevin thermostat). However what's the best choice for the barostat in Gromacs for such a system (Berendsen or Parinello-Rahman)? Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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] WCA potential
hi all, i am using a WCA potential and PME to calculate the non-bonded interactions of monomers of polyelectrolyte chains and counterions in solution. i use a table.xvg file where i have inserted the WCA potential (given values to x,f(x),f''(x),g(x),g''(x),h(x),h''(x) as is explained in the manual). is that the only way to insert the WCA potential in gromacs or i can do that automatically from the input file? Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ ___ 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] free energy calculations in charged systems
Hi all, i am working in polyelectrolyte solutions, and i would like to calculate the free energy for the polyectrolyte system (charged) to change to a neutral (non-charged) system. The question is if it feasible to use the PME electrostatics in gromacs for the above free-energy calculation. thanks Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ ___ 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] widom in Gromacs
Hi all, is it feasible to implement the widom method in Gromacs in a system of Lennard-Jones chains, in other words to insert a molecule chain and calculate the difference of DeltaU=U(N+1)-U(N) ? if it is feasible how this can be implemented thanks all of you regards __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] thermodynamic integration
Hi all , is it possible to do thermodynamic integration in Gromacs using non-linear scaling of the lamda paramerter? __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] biased potential in Gromacs
Hi everybody, i am working in vapor-liquid phase transitions of polyelectrolyte solutions is it possible to use a biased potential functon in Gromacs in order to overcome the free energy barrier between liquid-vapor phases? if yes, how this can be implemented in gromacs? thanks, in advance all of the people for their help. Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ 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] FENE potential
Hi, More than possible, it has already been done. Manual chapter 4.2.4, page 51. And please give me a very good reason why I now picked up the manual and looked for FENE, instead of you. My bad... :-P I assumed someone would read the available documentation resources before posting on this list. You'd think I'd learn, huh... Mark First of all in the gromacs manual 3.2, that i have on page 51 there is the LJ and Buckingham potential and in chapter 4.2.4 (page 58) the harmonic potential is discussed, so page 51 and chapter 4.2.4 talk about different things. Second the FENE potential has a form of VFENE = - k(R02/2)ln(1 - (r/R0)2), it is an anharmonic spring potential and has used extensiverly in coarse grains polymer models, it is harmonic only at the minimum Third Mark and Tsjerk you must be more careful, specific and polite in your answers you give, especially when you don't know what you are talking about, not try to get rid of someone, make sure first that you understand and have the right answer, otherwise it is better not to answer!___ 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] relative weight between the direct space sum and reciprocal space sum
HI, according to the 3.2 gromacs manual , the ewald_rtol parameter is the relative strength of the electrostatic interaction at the cut off, decreasing this gives a more accurate direct sum, but a less accurate reciprocal sum(p. 81). The beta parameter is the parameter that determines the relative weight between the direct sum and reciprocal sum(p.55) but i don't think you can set the beta parameter in gromacs ___ 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] implicit water model
HI from the time that epsilon(r) can not take a value different than 1, in order to simulate water as a continuum with a dielectric constant epsilon(r), I would like to know what kind of implicit water model GROMACS uses. Argyris Karatrantos ___ 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] LJ fluid
HI gromacs users, in order to simulate Argon fluid i use epsilon=m=sigma=1, so the parameters for the LJ are 4.000 4.000the question is what reduced time step (t*)is appropriate for MD, what coupling methods for temperature and pressure and what the value for nrexcl for the Ar atomsthanks in advance___ 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] error with mdrun
Hi , i am trying to do an mdrun and i get the following messageELAN_EXCEPTION @ --: 6 (Initialisation error) elan_init: Cant get capability from environmentAborted does anyone have any idea from where that error comes from ?___ 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] Fwd: compination rule
Hi, The warning message that i get is during grompp : Trying to add BuckingHam while the default nonbond type is LJ (SR) eventhough i get this warning message, the grompp works fine, and the mdrun too. Hi all, is it possible in the topology file to have (compination rule=1) and have under the [nonbond_params] both LJ potentials and Buckingham potentials. please let me know. i am doing that but i get some warnings after grompp procedure. thanks in advance ___ 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] Buckingham potential
Hi, what values the [defaults] parameters must have, ( non-bonded function type compination rule ) in order to be able to use Buckingham potential for the non-bonded interaction? Argyris Karatrantos ___ 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] nonbond_params
HI Gromacs users, my question is if i have to denote under the [nonbond_params] same non bonded atoms in a polymeric chain, such as C-C nonbonded interactions. i am giving the lennard jones parameters in the [atomtypes] for carbon(C). do i have to write again the nonbonded interaction of C-C under the [nonbond_params] section thanks in advance Argyris Karatrantos ___ 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
