[gmx-users] em.mdp

[Luca Mollica]

> Hi everyone,
> 
> I am rather new to Gromacs and would appreciate any input
> from anyone. 
> 
> I wanted to minimize my peptide first before going into md
> simulation. Do I prepare only one mdp file that comprises
> both em and md options, or do I prepare separate mdp files?
> And if the former is applicable, do I indicate the integrator
> only as md, while at the same time, having em options in the 
> same file?

Juraina,

this is a standard input file for minimization:



cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  1000
;
;       Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01
nstcomm             =  1
ns_type             =  grid
deltagrid           =  2
rlist               =  1.2
fourierspacing      =  0.12
pme_order           =  4.0
coulombtype         =  PME
rcoulomb            =  1.7
rvdw                =  1.2
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no



As you can see, it works only for minimization process: you can choose 
your favourite integration algorithm for this step, usually NOT md ....
As another message posted recently suggested, you have to use another 
input file for md, for instance:



cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
;
;	MD run, 1.5 ns
;
tinit               =  0.0
dt                  =  0.002
nsteps              =  750000   ; total 1500 ps.
nstcomm             =  1
nstxout             =  500
nstvout             =  1500
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10

ns_type             =  grid
coulombtype         =  PME
deltagrid           =  2
rlist               =  1.0
rcoulomb            =  1.1
fourierspacing      =  0.12
pme_order           =  4
rvdw                =  1.0

; Temperature coupling is on in two groups
Tcoupl              =  yes
tc-grps             =  Protein SOL
tau_t               =  0.1     0.1
ref_t               =  300     300

; Energy monitoring
energygrps          =  Protein  SOL
; Pressure coupling is now on
Pcoupl              =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0

; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529



that is a classical input (rather a basic & standard one ....) for 
simulation of a protein performed for 1.5 ns at constant pressure and 
temperature (300K, 1 bar isotropic).

Every detais you are interested in is explained on GROMACS user manual 
on line.
Another suggestion: usually I perform the following steps for MD simulation:

1. Minimization in vacuo
2. Minimization in the solvent
3. Restrained molecular dynamics
4. Unrestrained molecular dynamics

Step 3 is very important and critical for the success and goodness of 
your simlation, expecially with large systems simulation .....

Happy simulation!!

;-)

LM




*******************************************************************************************************

Luca Mollica
Dulbecco Telethon Institute (Biomolecular NMR Lab)

DIBIT-HSR,Via Olgettina 58, 1B4
20132 Milano (Italy)

Tel: 0039-02-26434824
Fax: 0039-02-26434153
E-mail: mollica.luca at hsr.it

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