[gmx-users] Pressure coupling and cut-off

[Yanmei Song]

Dear Justin:

Thanks for your response. Here is the complete my .mdp file:

title               =  pdm
cpp                 =  /lib/cpp
constraints         =  all_bonds
integrator          =  md
dt                  =  0.004   ; ps !
nsteps              =  2500000   ; total 10ns.
nstcomm             =  1
nstxout             =  50000
nstvout             =  50000
nstfout             =  0
nstlog              =  5000
nstenergy           =  5000
nstxtcout           =  25000
nstlist             =  10
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
rlist               =  1.4
rcoulomb            =  1.4
rvdw                =  1.4
fourierspacing      =  0.20
pme_order           =  4
ewald_rtol          =  1e-5
; Berendsen temperature coupling is on in one groups
Tcoupl              =  berendsen
tc_grps             =  PDM
tau_t               =  0.1
ref_t               =  300
; Energy monitoring
energygrps          =  PDM
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
;pc-grps            =  PDM
tau_p               =  1.0
ref_p               =  1.0
compressibility     =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  100000



On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Yanmei Song wrote:
>
>> Dear All:
>>
>> I have question about the pressure coupling. I have done a 10ns simulation
>> with 19800 atoms for 120 large molecules using the following pressure
>> coupling.
>>
>> Tcoupl              =  berendsen
>> tc_grps             =  PDM
>> tau_t               =  0.1
>> ref_t               =  300
>>
>> Pcoupl              =  berendsen
>> pcoupltype          =  isotropic
>> ;pc-grps            =  PDM
>> tau_p               =  1.0
>> ref_p               =  1.0
>> compressibility     =  4.5e-5
>>
>> Then I did g_energy for the last 3ns and got the results:
>>
>> Energy                      Average       RMSD     Fluct.      Drift
>>  Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Potential                    -98061          0          0    0.61668
>>  1850.04
>> Temperature                 303.561    109.602    109.602 0.000181791
>> 0.545372
>> Pressure (bar)               4.4884    11110.8    11109.8  -0.169835
>> -509.506
>>
>> For such a long run the pressure drift is still too much and seem hasn't
>> approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did
>> a similar system by using the same method. it just take 2 or 3ns to reach
>> the equilibrium. and the pressure is around 1.01after the run. The only
>> difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4
>> is too large to make the system running slower. Or the pressure coupling
>> method is not working well.  Anyone can give me any suggestions?
>>
>>
>>
> I think it will depend on the interplay of other parameters as well.
>  Posting a complete .mdp file may be more helpful.
>
> -Justin
>
>  --
>> Yanmei Song
>> Ph.D. Candidate
>> Department of Chemical Engineering
>> Arizona State University
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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