[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 option"The PME mesh contribution is subtracted from the user table by mdrun".

[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

[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 t

[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

[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

[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 P

[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 m

[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.

[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 ___

[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] 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 al

[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 lis

[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 relat

[gmx-users] relative weight of direct and reciprocal sum

Hi gromacs users, is there any way to set the beta parameter in gromacs which determines the relative weight of the direct and reciprocal sum for the long range electrostatics? is the fourier spacing the only way to control the reciprocal sum in the long range electrostatics? thanks a lot

[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] 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 adva

[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: Can't get capability from environmentAborted does anyone have any idea from where that error comes from ?___ gmx-users mailing list

[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@groma

[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

[gmx-users] compination rule

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 Argyris Karatrantos _

[gmx-users] proper dihedrals

Hi all, according to the manual the proper dihedrals are set, using in the topology file(top file) the inner two atoms of the dihedral. But how i can set the two following dihedrals, which have the same inner atoms C-O-C-H C-O-C-C but different external atoms, and of course different K values(KJ

[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 u

[gmx-users] dielectric constant

could you please tell me how we can change the dielectric constant epsilon(r) in the topology file. this constant has the default value of 1. thanks in advance Argyris Karatrantos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.or