[gmx-users] too_low_temperature

Dear all, I have a solvent (SW-water 519 molecules) and solute (NMA-peptide) system, whereby I coupled both of them seperately to a heath bath (Berendson , t=0.1 ps). Both heat baths have different T's, Solvent T=300K and Solute T=500K. The strange thing is that the temperature (g_energy)

Re: [gmx-users] density_SW_model

Hi David, I ran also a system with NMA+SPC,NMA+SPCE and other models, but the density was always reasonable (around 1 Kg/L). I used hereby the version 3.3.1. and all simulations were done in double precision including the simulations with SW water. I will also install the newer version 4.x

Re: [gmx-users] density_SW_model

Hello David, thank you for your response. Yes, this is the right mdp file. The total system contains also a small NMA molecule (6 atoms), which should not affect significantly the density (520 solvent molecules). Sang Min On Tue, 24 Feb 2009, David van der Spoel wrote: Sang-Min Park

[gmx-users] density_SW_model

Dear all, I ran a 1ns simulation in SW water (polarizable model) under NPT (P=1 bar , T=300 K) conditions. I checked the density and had a constant plateau value around 640 g/L , which is obviously too low. I used the flexible and rigid version (520 solvent molecules), with isotropic polar

[gmx-users] spc_flex reference

Hello everybody, does somebody know a reference concerning the "flexible SPC " modell which is used by GROMACS ? Thank you in advance Sang Min ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pleas

[gmx-users] DMSO_rigid_or_flex

First of all thank you Justin for your fast reply and the reference for the parameters in the dmso.itp file. And my thank goes of course also to the other people (Mark, Berk, David and so on ) who always finds time to answer the questions from a MD-beginner like me. I have some further quest

[gmx-users] dmso

Hello everybody, I would like to know about some references concerning the paramters in the dmso.itp file. Thank you for your time ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search t

gmx-users@gromacs.org

Dear gmx-users, does anybody know some references for C_v(heat cap) and viscosity values for SPCE and the flexible version of SPC water ? For SPC(rigid) , tip4p etc. are lot of literature references but I was not able to find C_v and viscosity for the above mentioned cases... Thank you for

[gmx-users] initial_configuration_sw_water

Hello everybody, I read somewhere that one can get the sw.gro file, by adding the shell and dummy particles (with the same coordinates as the oxygen) into the spc216.gro file. Is this right ? and when not how can I get the sw.gro file ? thank you for your time Sang Min _

[gmx-users] PME User

Dear all, I read in www.gromacs.org/gromacs/revisions/  in the report of David van der Spoel "Added support for a combination of PME and User determined coulomb potentials. The user has to take care that the combination of Coulomb and standard PME makes sense"  ( 8 Feb. 2005) I don't unders

[gmx-users] PME-User

Dear all, I have some questions concerning the usage of tables : 1. If one choose ' coloumbtype = User ' then GROMACS would calculate only the interaction according to the user specfied table within the specified cut off 'rcoloumb' and 'rlist'. The interaction beyond the cut offs would not

[gmx-users] user_defined_potential

Dear all, I have a question concerning the calculation of the Coulomb interaction energy with a user defined table. I generated a table where o n l y the coulomb interaction is multiplied by a factor a=2 and furthermore I used the following settings in the mdp file: energygrps= Protein

Re: [gmx-users] change coloumb interaction

? 2. I created the "table_Protein_SOL.xvg" file but GROMACS asks also for a file "table_Protein_SOL_Protein_SOL.xvg". What should be the content of this file ? Thank you in advance Sang Min > Sang-Min Park wrote: > > Dear all, > > > > I want to cha

[gmx-users] change coloumb interaction

Dear all, I want to change (for example : 2 times the 'normal' value) only the coloumb interaction between the solvent and a small peptide molecule. On the other hand the interaction SOL-SOL and peptide-peptide should be according to the standard given parameters of GROMACS. The change of

[gmx-users] hessian_matrix_from_ordered_trajectory

Dear all, I calculated the eigenvalues and eigenvectors from a small peptide with a closest water neighboorhood watersurrounding. To do this I generated a new trajectory with the command "trjorder" to order the watermolecules in a way so that they are close to the center of mass of the peptid