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

[HANNIBAL LECTER]

I am performing NPT here but this artifact is independent of whether one is
using NPT or NVT.


On Mon, Aug 19, 2013 at 11:42 AM, HANNIBAL LECTER <
hanniballecter13 at gmail.com> wrote:

> 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
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>| (410)
>> 706-7441
>>
>> ==============================**====================
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>
>