[gmx-users] Gromacs versions 4.0.5 and 4.5.4
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 19 04:28:04 CEST 2011
Itamar Kass wrote:
> Hi Sapna,
>
> It is a good question, but such of personal preferences. I found out
> that my simulations tend to crash more often when I am using 4.5.5. It
> might be the General-reaction -field I use or something else, I am not
> sure. Also, it seems I will not gain much from upgrading, so I stick to
> 4.0.7.
>
The general instabilities result from tweaks to the handling of temperature and
pressure coupling. Simply setting nsttcouple and nstpcouple to 1 during the
initial equilibration seems to give stable systems.
I'd say there are many reasons for upgrading. Tons of new features, bug fixes,
etc. But then too, that's my personal preference ;)
-Justin
> All this is not to say that 4.5.5 is not a good simulation package. It
> is a good and useful MD package, and I highly appreciate all the time
> and effort put into it.
>
> Best,
> Itamat
>
> PS, there are still people around using 3.3.3 or even 3.2.1, so I am not
> that behind.
>
> On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote:
>
>> Dear Itamar,
>>
>> Thank you for your response. Why did you prefer to stick to 4.0.7? Is
>> there something particularly difficult to transfer from 4.0.7 version
>> to 4.5 version?
>>
>> Sapna
>>
>> On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass <itamar.kass at monash.edu
>> <mailto:itamar.kass at monash.edu>> wrote:
>>
>> Hi Sapna,
>>
>> I had the same problem few weeks ago.
>>
>> Apparently, some parameters are different (eg. nstpcouple).
>>
>> Cheers,
>> Itamar
>>
>> PS I found out that I prefer to stick to 4.0.7.
>>
>>
>>
>>
>> On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote:
>>
>>> Dear All,
>>>
>>> I have a simulation set up for a mixture of carbon dioxide and
>>> water system which runs perfectly on Gromacs 4.0.5 version. I
>>> have run these simulations at different temperatures and
>>> pressures, from the same starting configuration and the
>>> simulation proceeds smoothly in the 4.0.5 version. However, when
>>> I use exactly the same files to run the simulation in 4.5.4
>>> version, the system crashes and writes out several pdb files. I
>>> was wondering if there is anything specific that has been changed
>>> between the two versions. I have pasted the mdp file of the
>>> simulations below. Any input will be much appreciated.
>>>
>>> MDP File
>>>
>>> title = 100% occupancy CO2 hydrate ; a string
>>> cpp = /lib/cpp ; c-preprocessor
>>> dt = 0.002 ; time step
>>> nsteps = 15000000 ; number of steps
>>> nstcomm = 10 ; reset c.o.m. motion
>>> nstxout = 0000 ; write coords
>>> nstvout = 0000 ; write velocities
>>> nstlog = 25000 ; print to logfile
>>> nstenergy = 500 ; print energies
>>> xtc_grps = OW_HW1_HW2_CO2
>>> nstxtcout = 1000
>>> nstlist = 10 ; update pairlist
>>> ns_type = grid ; pairlist method
>>> coulombtype = PME
>>> rvdw = 1.2 ; cut-off for vdw
>>> rcoulomb = 1.2 ; cut-off for coulomb
>>> rlist = 1.2 ; cut-off
>>> for coulomb
>>> DispCorr = EnerPres
>>> Tcoupl = Nose-Hoover
>>> ref_t = 270
>>> tc-grps = System
>>> tau_t = 0.5
>>> Pcoupl = Parrinello-Rahman
>>> Pcoupltype = semiisotropic ; pressure geometry
>>> tau_p = 1.0 1.0 ; p-coupoling time
>>> compressibility = 4.5e-5 4.5e-5 ; compressibility
>>> ref_p = 30.5 30.5 ; ref pressure
>>> gen_vel = yes ; generate
>>> initial vel
>>> gen_temp = 260 ; initial
>>> temperature
>>> gen_seed = 372340 ; random seed
>>> constraint_algorithm = shake
>>> constraints = all-bonds
>>>
>>> -------
>>>
>>>
>>> Thank you,
>>>
>>> Sincerely,
>>> Sapna
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>>
>> -----
>> "In theory, there is no difference between theory and practice.
>> But, in practice, there is." - Jan L.A. van de Snepscheut
>>
>> ===========================================
>> | Itamar Kass, Ph.D.
>> | Postdoctoral Research Fellow
>> |
>> | Department of Biochemistry and Molecular Biology
>> | Building 77 Clayton Campus
>> | Wellington Road
>> | Monash University,
>> | Victoria 3800
>> | Australia
>> |
>> | Tel: +61 3 9902 9376 <tel:%2B61%203%209902%209376>
>> | Fax: +61 3 9902 9500 <tel:%2B61%203%209902%209500>
>> | E-mail: Itamar.Kass at monash.edu <mailto:Itamar.Kass at monash.edu>
>> ============================================
>>
>>
>> --
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>>
>>
>>
>>
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>
> -----
> "In theory, there is no difference between theory and practice. But, in
> practice, there is." - Jan L.A. van de Snepscheut
>
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: Itamar.Kass at monash.edu <mailto:Itamar.Kass at monash.edu>
> ============================================
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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