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

HANNIBAL LECTER hanniballecter13 at gmail.com
Tue Aug 20 00:40:03 CEST 2013 

Interestingly, removing position restraints does not have much of an impact.


On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/19/13 11:58 AM, HANNIBAL LECTER wrote:
>
>> 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.
>>
>>
> What about changing the integrator to md?  What happens if you remove
> restraints while using sd?
>
> -Justin
>
>
>> 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
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.******edu <jalemkul at outerbanks.**
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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
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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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