On 8/7/16 1:21 PM, Dan Gil wrote:
In Gromacs/4.6, I used init to define the distance from the solvent COM
that the solute should be pulled to. Has it changed for Gromacs/5.1?
Nothing has changed except (1) syntax and (2) the ability to now apply multiple
restraints simultaneously. Everything with respect to setting references
distances, etc. is functionally the same.
What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
the solvent COM?
You can do that with "pull-coord1-init = X" and "pull-start = no" but this is
setting the reference distance to X, so if the initial coordinates are far from
that value, you're imparting a large force to start, which may not be stable.
It may work, but those initial steps are going to be dicey.
-Justin
Here is the section I think you are talking about also:
Pull group 1 'a_Cooh' has 1 atoms
Pull group 2 'SOL' has 5715 atoms
Number of degrees of freedom in T-Coupling group System is 44530.00
Pull group natoms pbc atom distance at start reference at t=0
1 1 0
2 5715 18540 3.011 nm 3.011 nm
On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 8/7/16 1:13 PM, Dan Gil wrote:
Hi,
I've made the change you suggested. The output file pullx.xvg has changed
from something like:
@ s0 legend "1"
@ s1 legend "1 dZ"
0.0000 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316
to this:
@ s0 legend "1"
@ s1 legend "1 dZ"
0.0000 3.01072 -3.01072
0.2000 2.98101 -2.98101
0.4000 2.94186 -2.94186
0.6000 2.95316 -2.95316
The second column should the COM of the solvent, the third column should
be
the position of a_Cooh. I am still wondering what is going on, since init
=
0.
pull-coord1-start = yes
grompp tells you what the reference distance is at the start; check to
make sure this is what you want it to be. pull-coord1-init = 0 means
"don't add anything extra to what is already there."
-Justin
On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 8/7/16 11:35 AM, Dan Gil wrote:
Hi,
The pullx.xvg file is returning the coordinates of the solvent, and not
the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I
specify:
pull-coord1-dim =N N Y
What is going on here?
Swap
pull-coord1-groups = 1 2
for
pull-coord1-groups = 2 1
to do what you had been doing in the previous version. You've inverted
the pull vector relative to the 4.6 settings.
-Justin
On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:
Hi All,
I'm having a similar problem and wouldn't mind some advice either. I
am
getting LINCS warnings on one cluster that I run my sampling on, but
the
pull-code works fine on other clusters we have access to, which is
making
me doubt the entire process.
Best regards,
Billy
On 7 August 2016 at 03:34, Dan Gil <dgil...@gmail.com> wrote:
Hi,
I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
.mdp
file that I am confused with.
I am pulling an atom of solute, indexed a_Cooh, towards the COM of
solvent.
This is a slab geometry, with the plane normal to the z-axis direction.
My
output (pullx.xvg) should contain the deltaZ value between the solute Z
coordinate and solvent COM z coordinate. With my current Gromacs/5.1
attempt, I don't think I am getting the correct results.
On Gromacs/4.6:
pull =umbrella
pull_geometry =distance
pull_dim =N N Y
pull_init1 =0
pull_k1 =100
pull_nstxout =100
pull_group0 =SOL
pull_group1 =a_Cooh
My attempt with Gromacs/5.1:
pull =yes
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type = umbrella
pull-coord1-geometry =distance
pull-coord1-groups = 1 2
pull-coord1-dim =N N Y
pull-coord1-start = yes
pull-coord1-init =0
pull-coord1-k =1000
pull-print-components = yes
pull_nstxout =100
Best Regards,
Dan
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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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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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