[gmx-users] Chloride parameters in ffgmx

[hugo verli]

Hi,

I made a chloroform box and simulated it in NVT for 500ps and in NPT for
5500ps. The volume and density are quite stable in MD trajectory. However, de
obtained average density is 5.51846e+02, when it should be around 1.489g/cm3.
Here is my .mdp file:


title               =  Yo
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  all-bonds
integrator          =  md
tinit               =  3000.0
dt                  =  0.002    ; ps !
nsteps              =  1500000  ; total 3000 ps.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
optimize_fft        =  yes
pme_order           =  4
ewald_rtol          =  1e-5
DispCorr            =  EnerPres
; Berendsen temperature coupling is on in four groups
Tcoupl              =  berendsen
tc-grps             =  CCL
tau_t               =  0.1
ref_t               =  293
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 100 K.
gen_vel             =  no
gen_temp            =  293.0
gen_seed            =  173529

The charges were obtained from Ab-initio calculations and the topology for the
chloroform made in PRODRG site.

Any suggestion? Could this error be due to atomic charges or to van der Waals
parameters (form chloride ion and not for covalent bound chlorine)?

Thanks in advance for any help,

Hugo.

> Hi,
> 
> I tried to make a chloroform box with gromacs. I follow a previous suggestion
> described here in this list to use the PRODRG site to obtain the 
> topology file for solvent molecule. However, looking the chlorine 
> parameters choosed by PRODRG site I found that it correspond to 
> chloride ion. I did not found any parameters in ffgmx file referent 
> to covalented bound chlorine.Should I expect a reasonable MD 
> trajectory using these parameters? 
> 
> I have to use the ffgmx because I want to analyse the conformational 
> profile of a ligand in this solvent.  
> 
> MSc. Hugo Verli
> Centro de Biotecnologia
> Universidade Federal do Rio Grande do Sul
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MSc. Hugo Verli
Centro de Biotecnologia
Universidade Federal do Rio Grande do Sul