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.

Reply via email to