On 4/23/15 10:34 AM, Jianhui Tian wrote:
Date: Wed, 22 Apr 2015 19:23:32 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0
Message-ID: <55382d74.5070...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 4/22/15 4:59 PM, Jianhui Tian wrote:
Date: Wed, 22 Apr 2015 16:05:18 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0
Message-ID: <5537fefe.6020...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 4/22/15 3:54 PM, Jianhui Tian wrote:
Dear Users,
I am trying to do a umbrella pulling of one lipid out of a bilayer
using
umbrella sampling code. In Gromacs 5.0, there is a big change in
umbrella
sampling implementation. I set my pull parameters like this:
pull = umbrella
pull_geometry = cylinder ; Pull in the direction of pull-vec.
pull_coord1_vec = 0.0 0.0 -1.0
pull_r1 = 1.0
pull_r0 = 1.5
pull_start = yes
pull_ngroups = 2
pull_ncoords = 1
pull_coord1_groups = 1 2
pull_group1_name = PullLipid ; one lipid that I want to pull out
pull_group2_name = RefLipids ; lipids on the other leaflet of
bilayer
pull_coord1_rate = 0.001 ; 0.001 nm per ps = 1 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
When I have a small system, it can work but had and following error and
stopped:
Fatal error:
Distance between pull groups 1 and 2 (2.707004 nm) is larger than 0.49
times the box size (2.758373).
You might want to consider using "pull-geometry = direction-periodic"
instead.
I guess this is due to a small box size (about 5.52 nm in x and y).
Then I double the system size and redo the umbrella sampling. I got the
following message with grompp:
########################################################
Pull group natoms pbc atom distance at start reference at t=0
1 130 23335
2 3136 38129 -nan -nan
########################################################
Something is messed up in the input coordinates. If the reference
distance is
"not a number," then you need to diagnose what it is you've done to the
coordinates before doing anything else.
-Justin
Thanks, Justin.
But, what do you mean by coordinates messed up?
No idea, but you should never see "nan" if everything is sensible. There
are a
bunch of possibilities, but the ones I can think of would cause a fatal
error.
I have a gro file for generating the tpr for umbrella pulling.
The same GRO file can be used to generate a tpr file for normal MD run
without any problems.
OK, so it's specific to something being interpreted by the pull code. Try
varying some settings to see if it illuminates anything. Otherwise, you
need to
upload all of your files somewhere (as well as a list of all your commands,
exactly as you gave them) for us to look into it.
-Justin
--
==================================================
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
==================================================
Hi Justin,
My complete mdp file is as follows:
include =
define =
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 2500000
nstlog = 5000
nstxout = 5000
nstvout = 5000
nstxout-compressed = 5000
nstenergy = 5000
energygrps = Lipids Water
;
cutoff-scheme = Verlet
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
fourierspacing = 0.12
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 0.8
rvdw = 1.2
;
tcoupl = v-rescale ;Nose-Hoover
tc_grps = Lipids Water
tau_t = 1.0 1.0
ref_t = 323.15 323.15
ld-seed = 1454538035
;
pcoupl = berendsen ;Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = no
lincs_order = 4
;
nstcomm = 100
comm_mode = linear
comm_grps = System
;
refcoord_scaling = com
;
gen_vel = no
gen_temp = 323.15
;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;
;;; Pull Code ;;;
;;; Steered MD ;;;
;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;
pull = umbrella
pull_geometry = cylinder ; Pull in the direction of pull-vec.
pull_coord1_vec = 0.0 0.0 -1.0
pull_r1 = 1.0
pull_r0 = 1.5
pull_start = yes
pull_ngroups = 2
pull_ncoords = 1
pull_coord1_groups = 1 2
pull_group1_name = PullLipid
pull_group2_name = RefLipids
pull_coord1_rate = 0.001 ; 0.001 nm per ps = 1 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
I used a grompp command to generate tpr file for umbrella pulling:
grompp -f pull.mdp -c GRO -p TOP -n NDX -o pull.tpr
Then, I used mdrun to do the umbrella pulling:
mdrun -s pull.tpr ...
I do not know whether this will be enough for pinning the problem.
Otherwise, I can upload the files if there is a place for doing so.
Upload your files using whatever service you like. There's nothing from the
above information that indicates a problem.
-Justin
--
==================================================
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
==================================================
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