Hi, Thanks for your help, Justin!
Regards, Mahsa On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/25/18 10:15 AM, Mahsa wrote: > >> Dear Justin, >> >> Thank you for your reply! >> >> In general, is it a good approach to first use steep algorithm for EM and >> then to further minimize do EM with cg algorithm, on the output structure? >> > > I usually don't find multiple steps of EM needed in most cases, but > occasionally. The purpose of EM is to find a plausible starting point for > the simulation - you can never know if you're in the global minimum so it's > a bit of working in the dark, anyway. But the gradient (max force) reports > on that. > > Could you please comment on my question about the mdp files and pbc as >> well? Actually, you mentioned here: >> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users >> /2017-February/111219.html >> >> that for one chain of polymer in vacuum, pbc should not be considered. So, >> for my simulation, in the first step I have one chain in vaccum and >> eventually I want to pack the whole box with polymer chains and ions, >> should I use pbc or not and which of the mdp files in my first post is >> correct? >> > > If you're working in the condensed phase, you need finite cutoffs, PME, > and PBC. > > -Justin > > > Regards, >> Mahsa >> >> On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 2/25/18 9:26 AM, Mahsa wrote: >>> >>> Dear Mark, >>>> >>>> Thank you for your reply. However, this is not clear for me yet since I >>>> read this in the tutorial from Justin: >>>> >>>> "There are two very important factors to evaluate and determine if EM >>>> was >>>> successful. The first is the potential energy (printed at the end of the >>>> EM >>>> process, even without -v). Epot should be negative. The second important >>>> feature is the maximum force, Fmax, the target for which was set in >>>> minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater >>>> than >>>> 1000 kJ mol-1 nm-1." >>>> >>>> So I don't know whether it is correct to continue a simulation which >>>> gives >>>> positive potential energy after the energy minimisation or not? >>>> >>>> And also as I mentioned in my first post (the two different mdp files), >>>> I >>>> don't know if I should consider pbc or not, in my simulation. >>>> >>>> Unfortunately, I didn't understand your answer to my previous questions. >>>> Do >>>> you mean that the steep integrator is not good to do energy minimization >>>> for this type of simulation? >>>> >>>> Would you please help me to fix these problems? >>>> >>>> There is no problem. You're just comparing apples and oranges. >>> >>> The tutorial system is a simple protein solvated by lots of water. The >>> potential energy function is the sum of bonded and nonbonded terms. In an >>> aqueous protein system, the nonbonded terms (particularly water-water >>> electrostatics) dominate the potential energy via favorable hydrogen bond >>> interactions. The internal (bonded) parameters for all the other species >>> are small in magnitude, by comparison, so the nonbonded terms dominate >>> and >>> you get a negative potential energy. >>> >>> In your case, you have comparatively weak nonbonded terms and larger >>> bonded terms, such that the potential energy function is dominated by >>> internal energy, which is by definition, positive. >>> >>> This is not an indication that anything is wrong with the algorithms >>> used. >>> >>> -Justin >>> >>> >>> Regards, >>> >>>> Mahsa >>>> >>>> On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham <mark.j.abra...@gmail.com >>>> > >>>> wrote: >>>> >>>> Hi, >>>> >>>>> Even if there are minima on the surface that have negative energy >>>>> (which >>>>> will depend how the model was developed, which you should look into) >>>>> there's no reason to expect an arbitrary starting configuration will >>>>> find >>>>> one after a steepest descent search. A tangled pile of strings will >>>>> stay >>>>> tangled. >>>>> >>>>> Mark >>>>> >>>>> On Fri, Feb 23, 2018, 23:28 Mahsa E <ebadi.ma...@gmail.com> wrote: >>>>> >>>>> Hello, >>>>> >>>>>> I want to simulate a box of polymer (32 chains) with salt. I started >>>>>> with >>>>>> one chain of the polymer in the box. However, after the energy >>>>>> minimisation, the energy is still positive. I found the discussion in >>>>>> the >>>>>> link below very similar to the problem I have: >>>>>> >>>>>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users >>>>>> /2017-February/111219.html >>>>>> >>>>>> and tried the tips from Justin in the link but I still get positive >>>>>> >>>>>> energy. >>>>> >>>>> This is my first MDP file: >>>>>> >>>>>> define = >>>>>> integrator = steep >>>>>> nsteps = -1 >>>>>> nstcgsteep = 10 >>>>>> constraints = none >>>>>> lincs_order = 8 >>>>>> emtol = 20 >>>>>> emstep = 0.01 >>>>>> comm-mode = Linear >>>>>> nstcomm = 1 >>>>>> nstcalcenergy = 1 >>>>>> ; Output frequency for energies to log file and energy file >>>>>> nstlog = 1 >>>>>> nstenergy = 1 >>>>>> ns_type = grid >>>>>> cutoff-scheme = verlet >>>>>> coulombtype = PME >>>>>> nstlist = 10 >>>>>> rlist = 1.0 >>>>>> rcoulomb = 1.0 >>>>>> rvdw = 1.0 >>>>>> Tcoupl = no >>>>>> Pcoupl = no >>>>>> gen_vel = no >>>>>> nstxout = 1 >>>>>> pbc = xyz >>>>>> >>>>>> and this is the second one which I tried to follow the tips from the >>>>>> link >>>>>> mentioned above: >>>>>> >>>>>> define = >>>>>> integrator = steep >>>>>> nsteps = -1 >>>>>> nstcgsteep = 10 >>>>>> constraints = none >>>>>> lincs_order = 8 >>>>>> emtol = 20 >>>>>> emstep = 0.01 >>>>>> comm-mode = Linear >>>>>> nstcomm = 1 >>>>>> nstcalcenergy = 1 >>>>>> ; Output frequency for energies to log file and energy file >>>>>> nstlog = 1 >>>>>> nstenergy = 1 >>>>>> ns_type = grid >>>>>> cutoff-scheme = group >>>>>> coulombtype = cut-off >>>>>> nstlist = 0 >>>>>> rlist = 0 >>>>>> rcoulomb = 0 >>>>>> rvdw = 0 >>>>>> Tcoupl = no >>>>>> Pcoupl = no >>>>>> gen_vel = no >>>>>> nstxout = 1 >>>>>> pbc = no >>>>>> >>>>>> My questions are: >>>>>> >>>>>> - I'm not sure if either of these MDP files are correct for the system >>>>>> >>>>>> I'm >>>>> >>>>> trying to simulate? >>>>>> >>>>>> - Why energy is positive in this simulation? Is there something >>>>>> fundamentally wrong in the simulation which I'm not aware of? >>>>>> >>>>>> Regards, >>>>>> Mahsa >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>> >>>>>> -- >>>>>> >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at http://www.gromacs.org/ >>>>> Support/Mailing_Lists/GMX-Users_List before posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>>> >>>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> ================================================== >>> >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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