[gmx-users] Gromacs versions 4.0.5 and 4.5.4
Sapna Sarupria
sapna.sarupria at gmail.com
Wed Oct 19 23:40:56 CEST 2011
Hello,
I did change nsttcouple and nstpcouple but the simulations that run in 4.0.5
are still crashing in 4.5.4. I think it is related to constraints but I am
unable to figure out exactly what is different. I have pasted both my
topology and mdp (updated for 4.5.4) files. Any ideas? I have read through
the manual and it seems like the mdp files does not need any changes, but
perhaps I am missing something.
Thank you for your help!
Sincerely,
Sapna
@@@@ MDP File @@@@
title = 100% occupancy CO2 hydrate ; a string
cpp = /lib/cpp ; c-preprocessor
integrator = md
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
nsttcouple = 1
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
nstpcouple = 1
gen_vel = yes ; generate initial vel
gen_temp = 260 ; initial temperature
gen_seed = 372340 ; random seed
constraint_algorithm = shake
constraints = all-bonds
@@@@ end MDP File @@@@
@@@@ Topology file @@@@
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 1.0 1.0
[ atomtypes ]
; name mass charge ptype sigma epsilon
; Water parameters are those of Vega TIP4P/Ice Model
OWT4 15.9994 0.0000 A 0.31668 0.882164429
HW 1.008 0.5897 A 0.000 0.000
MW 0.000 -1.1794 V 0.000 0.000
; TraPPE rigid
M2 22.0000 0.00 A 0.000 0.000000 ;
M1 22.0000 0.00 A 0.000 0.000000 ;
DO 00.0000 -0.35 V 0.305 0.656806 ; oxygen
DC 00.0000 0.70 V 0.280 0.224478 ; carbon
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
1 OWT4 1 SOL OW 1 0.0000
2 HW 1 SOL HW1 1 0.5897
3 HW 1 SOL HW2 1 0.5897
4 MW 1 SOL MW 1 -1.1794
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 502416.0
1 3 1 0.09572 502416.0
2 3 1 0.15139 502416.0
[ exclusions ]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
; The position of the dummy is computed as follows:
;
; O
;
; D
;
; H H
;
; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
; 0.01577 nm / [ cos (52.26 deg) * 0.09572 nm ]
; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
[ virtual_sites3 ]
; Dummy from funct a b
4 1 2 3 1 0.13458335087 0.13458335087
[ moleculetype ]
; molname nrexcl
TIP 2
[ atoms ]
1 OWT4 1 TIP OW 1 0.0000
2 HW 1 TIP HW1 1 0.5897
3 HW 1 TIP HW2 1 0.5897
4 MW 1 TIP MW 1 -1.1794
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 502416.0
1 3 1 0.09572 502416.0
2 3 1 0.15139 502416.0
[ exclusions ]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
[ virtual_sites3 ]
; Dummy from funct a b
4 1 2 3 1 0.13458335087 0.13458335087
[ moleculetype ]
; molname nrexcl
CO2 2
[ atoms ]
1 M1 1 CO2 M1 1 0.00 22.00
2 M2 1 CO2 M2 1 0.00 22.00
3 DC 1 CO2 CO 1 0.70 0.000
4 DO 1 CO2 OC1 1 -0.35 0.000
5 DO 1 CO2 OC2 1 -0.35 0.000
[ constraints ]
1 2 1 0.19785026
[ virtual_sites2 ]
; ai aj ak funct a
3 1 2 1 0.50
4 1 2 1 -0.086327900
5 1 2 1 1.086327913
[ exclusions ]
3 4 5
4 5 3
5 4 3
[ system ]
Hydrate with cages filled with carbon dioxide
[ molecules ]
SOL 2944
CO2 512
TIP 3641
@@@@ End topology file @@@@
On Wed, Oct 19, 2011 at 7:17 AM, Sapna Sarupria <sapna.sarupria at gmail.com>wrote:
> 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
>>>>> -- gmx-users mailing list gmx-users at gromacs.org
>>>>> <mailto:gmx-users at gromacs.org>
>>>>>
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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>
>>
>> ==============================**==========
>>
>> --
>>
>
--
Sapna Sarupria
Post-doctoral Researcher
Princeton University
New Jersey 08540
U.S.A.
Life isn't about finding yourself. Life is about creating yourself. --
George Bernard Shaw.
Dare to Dream
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