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

[HANNIBAL LECTER]

I usually use 1.0 for my systems and I get the correct values for the
temperatures. If I couple it as a system, the low T-CNT yields a different
value than the target 300K.


On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
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>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
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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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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