[gmx-users] Gromacs versions 4.0.5 and 4.5.4
Sapna Sarupria
sapna.sarupria at gmail.com
Wed Oct 19 13:17:55 CEST 2011
Dear Itamar and Justin,
Thank you for your responses. I will make the changes to the mdp files and
see how easy or hard it is to make the shift from 4.0.5 to 4.5.
Sincerely,
Sapna
On Tue, Oct 18, 2011 at 10:28 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>>>>
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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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>>
>> -----
>> "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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
> --
>
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