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 <[email protected]>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 <[email protected]>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 >>>> <[email protected]<mailto: >>>> [email protected]**>> 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 [email protected] >>>>> <mailto:[email protected]> >>>>> >>>>> >>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> Please search the archive at >>>>> >>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 [email protected] >>>>> <mailto:gmx-users-request@**gromacs.org<[email protected]> >>>>> >. >>>>> >>>>> Can't post? Read >>>>> http://www.gromacs.org/**Support/Mailing_Lists<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 <tel:%2B61%203%209902%209376> >>>> | Fax: +61 3 9902 9500 <tel:%2B61%203%209902%209500> >>>> | E-mail: [email protected] <mailto:[email protected]**> >>>> >>>> ==============================**============== >>>> >>>> >>>> -- >>>> gmx-users mailing list [email protected] >>>> <mailto:[email protected]> >>>> >>>> >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> Please search the archive at >>>> >>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 [email protected] >>>> <mailto:gmx-users-request@**gromacs.org<[email protected]> >>>> >. >>>> >>>> Can't post? Read >>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> >>>> >>>> >>>> >>>> -- >>>> gmx-users mailing list [email protected] <mailto: >>>> [email protected]> >>>> >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<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 [email protected]. >>>> Can't post? Read >>>> http://www.gromacs.org/**Support/Mailing_Lists<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: [email protected] <mailto:[email protected]**> >>> ==============================**============== >>> >>> >> -- >> ==============================**========== >> >> 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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