Thanks :)

On 1 December 2016 at 23:40, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 12/1/16 4:53 AM, Billy Williams-Noonan wrote:
>
>> Also, you may want to check that your rcoulomb and rvdw values are
>> correct...  Didn't look at your mdp files until just now.  Why are they
>> set
>> to zero?
>>
>>
> Vacuum simulations are done with infinite cutoffs (rlist=rcoulomb=rvdw=0)
> and no PBC.
>
> -Justin
>
> On 29 November 2016 at 16:56, Billy Williams-Noonan <
>> billy.williams-noo...@monash.edu> wrote:
>>
>> My PMF curves look similar to that.  What you're seeing towards the end of
>>> that curve is either an artifact of the algorithms used to model the
>>> system, a very minor sampling problem, or a mix of both.  Your Gaussians
>>> may be split because they are bi-modal and the most energetically
>>> favourable position around your constraint is in two places.  Try having
>>> a
>>> look at your individual umbrella windows to figure out what's going on.
>>> :)
>>>
>>> Cheers,
>>>
>>> Billy
>>>
>>> On 29 November 2016 at 15:20, Shi Li <sli...@g.uky.edu> wrote:
>>>
>>> Dear Gromacs users,
>>>>
>>>> I posted this question a few days ago, but still couldn’t solve it. This
>>>> problem has bothered my for a long time, so I am reposting this for
>>>> help.
>>>>
>>>> I am currently doing some PMF simulations for two small molecular types
>>>> in vacuum. I applied an energy minimization, a NVT equilibrium and a
>>>> production run on my system. Following are the mdp files for each. I
>>>> used a
>>>> commend in my run script to change the Window in pull_coord1_init in the
>>>> pull code for each sample window.
>>>>
>>>> Energy minimization
>>>> ---
>>>> integrator               = steep
>>>> nsteps                   = 20000
>>>>
>>>> nstenergy                = 500
>>>> nstlog                   = 500
>>>> nstxout-compressed       = 1000
>>>>
>>>> cutoff-scheme            = group
>>>>
>>>> coulombtype              = Cut-off
>>>> rcoulomb                 = 0
>>>>
>>>> vdwtype                  = Cut-off
>>>> rvdw                     = 0
>>>> rlist                    = 0
>>>> pbc                      = no
>>>>
>>>> ; Pull code
>>>> pull             = umbrella
>>>> pull_geometry    = distance
>>>> pull_start       = no
>>>> pull-ncoords     = 1
>>>> pull_group1_name = ADT1
>>>> pull_group2_name = ADT2
>>>> pull-coord1-groups = 1 2
>>>> pull_coord1_init = WINDOW
>>>> pull_coord1_rate = 0.0
>>>> pull_coord1_k = 5000
>>>>
>>>> —
>>>> NVT
>>>> ----
>>>> integrator               = md
>>>> dt                       = 0.002     ; 2 fs
>>>> nsteps                   = 500000    ; 1.0 ns
>>>>
>>>> nstenergy                = 200
>>>> nstlog                   = 2000
>>>> nstxout-compressed       = 10000
>>>>
>>>> continuation             = yes
>>>> constraint-algorithm     = lincs
>>>> constraints              = h-bonds
>>>>
>>>> cutoff-scheme            = group
>>>> rlist                    = 0
>>>>
>>>> rcoulomb                 = 0
>>>>
>>>> rvdw                     = 0
>>>> pbc                      = no
>>>> tcoupl                   = V-rescale
>>>> tc-grps                  = System
>>>> tau-t                    = 2.0
>>>> ref-t                    = 298.15
>>>> nhchainlength            = 1
>>>>
>>>> ; Pull code
>>>> pull             = umbrella
>>>> pull_geometry    = distance
>>>> ;pull_dim         = N N Y
>>>> pull_start       = no
>>>> pull-ncoords     = 1
>>>> pull_ngroups     = 2
>>>> pull_group1_name = ADT1
>>>> pull_group2_name = ADT2
>>>> pull-coord1-groups = 1 2
>>>> pull_coord1_init = WINDOW
>>>> pull_coord1_rate = 0.0
>>>> pull_coord1_k = 5000
>>>>
>>>> ——
>>>> Production run:
>>>> ----
>>>> integrator               = md
>>>> dt                       = 0.002   ; 2 fs
>>>> nsteps                   = 10000000   ; 20.0 ns
>>>>
>>>> nstenergy                = 5000
>>>> nstlog                   = 5000
>>>> nstxout-compressed       = 5000
>>>>
>>>> continuation             = yes
>>>> constraint-algorithm     = lincs
>>>> constraints              = h-bonds
>>>>
>>>> cutoff-scheme            = Group
>>>>
>>>> rcoulomb                 = 0
>>>> rlist                    = 0
>>>>
>>>> rvdw                     = 0
>>>> pbc                      = no
>>>>
>>>> tcoupl                   = V-rescale; Nose-Hoover
>>>> tc-grps                  = System
>>>> tau-t                    = 2.0
>>>> ref-t                    = 298.15
>>>> nhchainlength            = 1
>>>>
>>>> ; Pull code
>>>> pull             = umbrella
>>>> pull_geometry    = distance
>>>> pull_start       = no
>>>> pull-ncoords     = 1
>>>> pull_ngroups     = 2
>>>> pull_group1_name = ADT1
>>>> pull_group2_name = ADT2
>>>> pull-coord1-groups = 1 2
>>>> pull_coord1_init = WINDOW
>>>> pull_coord1_rate = 0.0
>>>> pull_coord1_k = 5000
>>>>
>>>> ———
>>>> I have a very strange profile and histogram. I uploaded to these links.
>>>>
>>>> PMF: https://www.dropbox.com/s/i10hn1p30w2j71r/F-anti-adt.eps?dl=0
>>>> HISTO: https://www.dropbox.com/s/1xi9i4cj60g97n2/F-anti-histo.eps?dl=0
>>>>
>>>> The molecule is about 1.5 nm long, so the smooth profile before 1.5 nm
>>>> looks fine, but I don’t understand why the profile had this fluctuation
>>>> after 1.5 nm and the histogram seems to have some split peaks after this
>>>> length. Can anyone tell me why this happened? Is there something wrong
>>>> in
>>>> my mdp file or something wrong in my topology? I have used this similar
>>>> mdp
>>>> files for my other types of molecular systems and the results were
>>>> fine. So
>>>> it is really confused me now.
>>>>
>>>> I appreciate for any help! Thanks!
>>>>
>>>> Shi
>>>>
>>>>
>>>>
>>>> --
>>>> 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.
>>>>
>>>
>>>
>>>
>>>
>>> --
>>> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>>>
>>> *LinkedIn Profile
>>> <http://www.linkedin.com/profile/preview?locale=en_US&trk=
>>> prof-0-sb-preview-primary-button>
>>> **|*   +61420 382 557 <+61%20420%20382%20557>
>>>
>>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
>>> Royal Parade, Parkville, 3052
>>>
>>>
>>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> --
> 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.
>



-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
-- 
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.

Reply via email to