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

Justin Lemkul jalemkul at vt.edu
Wed Aug 21 22:24:57 CEST 2013 


On 8/21/13 4:22 PM, HANNIBAL LECTER wrote:
> I am not sure what is the problem with using NPT, constraints and
> freezegroups. Unless there is some fundamental issue (which I cannot think
> of) one should in principle be able to run NPT with the CNT system by
> freezing the CNT group. I am using sd with LINCS to constraint the bonds.
> However, if md is used with SHAKE the system crashes with segmentation
> fault. Does anyone have any idea as to what could be the problem?
>

Changing multiple settings simultaneously is not helpful; change one variable at 
a time to see what the effect is.  For instance, change sd to md but leave the 
constraints as LINCS.  SHAKE is less stable, anyway.

I already explained why one cannot safely use freezegrps with NPT.  There are 
numerous discussions in the list archive about the negative consequences. 
grompp used to warn about this combination, hopefully it still does.

-Justin

>
> On Mon, Aug 19, 2013 at 6:40 PM, HANNIBAL LECTER <hanniballecter13 at gmail.com
>> wrote:
>
>> 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.**
>>>>>>> umaryland.edu <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 <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 <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

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