[gmx-users] NPT, freezegroups and Position Restraints.

[HANNIBAL LECTER]

Thanks Justin.

I am not sure how it is fundamentally incompatible. Especially with
refcoord-scaling = com. Can you please provide with some more input on that?


The outputs are from g_energy.

Here is the .mdp file.

define             =  -DPOSRES_CNT
constraints         =  all-bonds
pbc                 =  xyz
integrator          =  sd
ld_seed             =   215546
dt                  =  0.002    ; ps !
nsteps              =  50000    ; 50 ns
;nsteps                     = 125000    ; 250 ps
nstcomm             =  10
nstcalcenergy       =  10
nstxout             =  0
nstxtcout           =  5000 ;every 10 ps
nstvout             =  100
nstfout             =  0
nstlog              =  1000
nstenergy           =  1000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
vdwtype             =  cut-off
rvdw                =  1.0
coulombtype         =  pme
rcoulomb            =  1.0
fourierspacing      = 0.12
pme_order           = 4
ewald_rtol          = 1e-5
optimize_fft        =  yes
tc-grps             =  Protein CNT SOL
tau_t               =  1.0 1.0 1.0
ref_t               =  300.000 300 300
;freezegrps          = CNT
;freezedim           = Y Y Y
; Energy monitoring
energygrps          =  CNT Protein SOL
; energygrp-excl     = CNT CNT
; Isotropic pressure coupling is now on
Pcoupl              = Berendsen
refcoord-scaling    = com
Pcoupltype          = isotropic
tau_p               = 5
compressibility     = 4.5e-5
ref_p               = 1.0
gen_vel             =  yes
gen_temp            =   300.000
gen_seed            =    981487



On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/19/13 11:32 AM, HANNIBAL LECTER wrote:
>
>> Hi,
>>
>> I have been performing NPT simulations with CNT, Protein and water.
>> However, when I freeze the CNT, the system crashes with segmentation
>> fault.
>>
>>
> That is to be expected.  Frozen atoms and pressure coupling are
> fundamentally incompatible.
>
>
>  If I use position restraints, the temperature of the system is lower than
>> what it is expected to be. I am using sd coupling.
>>
>> If I couple the protein, CNT and SOL separately, the temperature of the
>> peptide is lower than 300K (~395K) while the temperature of the CNT is
>> 157K. The target temperature is 300K in all cases. Can any please explain
>> why such discrepancies are occurring?
>>
>>
> Are these temperatures from g_energy or g_traj?  Can you please post a
> full .mdp file?
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
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