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

[Justin Lemkul]

On 8/19/13 11:42 AM, HANNIBAL LECTER 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 refcoord-scaling option doesn't matter with frozen groups.  Anything that is 
frozen, by definition, never has its position updated.  Under the influence of 
pressure coupling, other particles around the frozen group can have their 
positions scaled and thus collide with the frozen group, which has remained in 
its original location.

>
> The outputs are from g_energy.
>

OK, good.

> 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

Note that tau_t is the inverse friction constant, not the "normal" coupling 
constant.  In this case, I don't know what appropriate values are, especially if 
one of your groups is restrained.  The manual advises a value of 2.0, so at 
least try that.  Otherwise, try coupling the System as a whole or use a 
different integrator (i.e., md) to try to figure out the origin of the problem.

-Justin

> 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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-- 
==================================================

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 | (410) 706-7441

==================================================