[gmx-users] Gromacs versions 4.0.5 and 4.5.4
Itamar Kass
itamar.kass at monash.edu
Wed Oct 19 04:22:38 CEST 2011
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.
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> 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
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> -----
> "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
> ============================================
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-----
"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
============================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111019/500a71f7/attachment.html>
More information about the gromacs.org_gmx-users
mailing list