shahid nayeem wrote:
I ran normal MD and it runs fine. Today I used six 10ps MD keeping
temperature 300 K and each time gradually increasing pressure from 1
bar to 5 bar to 25, 50, 75 and then 100bar. It all ran successfully.
Thereafter doing simulated annealing for cooling and heating and
equilibration. It all ran successfully without any LINC warning. But
should I trust this box because you said parameters assigned by prodrg
are none-sense.
I've made my thoughts on that matter pretty clear, I think. You have to justify
to reviewers that your parameters are accurate. We recently published a paper
detailing the artifacts that can arise from using unrefined PRODRG topologies;
the incorrect results are quite pronounced. You need to derive suitable charges
in conjunction with sensible charge groups. Garbage in, garbage out.
-Justin
shahid Nayeem
On Wed, Feb 9, 2011 at 5:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
shahid nayeem wrote:
Hi Justin
Thanks a lot.
I tried doing energy minimization and th lowering emtotal to 200 and
the system converged to
Steepest Descents converged to Fmax < 200 in 1411 steps
Potential Energy = -3.9063050e+05
Maximum force = 1.3442458e+02 on atom 927
Norm of force = 1.4758101e+01
OK, so energy minimization was fine.
For equilibration of solvation box I am following a biophys j paper
in which protocol for urea box preparation is given. A simulated
annealing under high pressure (ref_p=100) to cool system from 300 to
0K thereafter heating back to 300K at ref_p=1. Again 1ns MD at same
condition. If this way is harsh treatment of system then suggest me
the way out.
My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp
are attached with this mail
There's nothing obviously wrong with the .mdp file. Have you tried running
"normal" MD to check for stability? I suggested that before, and I'm still
curious.
Also, your CHAPS topology makes no sense. The haphazard charge assignment
and nonsensical charge groups indicate to me that PRODRG has done its usual
job of assigning funny parameters. Even if you could get the simulations to
run, they shouldn't be trusted, and bad parameters could well be the source
of your problem. Parameterization is time-consuming and difficult, but so
is generated quality, usable data :)
-Justin
Shahid Nayeem
On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
shahid nayeem wrote:
Please tell me where I am wrong. I downloaded pdb of chaps and used
prodrg server to get .itp and .gro file. Then I checked .itp for any
missing charge and I found it correct. Then I created 6.0x6.0x6.0 box
PRODRG doesn't have a problem of missing charges. It provides
notoriously
incorrect charges.
with genbox inserting 7 molecules of chaps.gro. Then again using
genbox and -maxsol I put 510 spc.itp in the box to get a density
approaching 1. Then I did steepest descent energy minimization with
constraints = none, for emtotal=2000 and emstep=3000. Up to this the
These settings make no sense. An emtol of 2000 is very high, and emstep
of
3000 is total nonsense. How well did you EM converge? What were the
values
of the potential energy and maximum force?
gromacs runs fine. when I start simulated annealing for cooling at
high pressure with constraint = all_bonds the programme gives fatal
error linc warning and stops. If I do energy minimization with
constraint =all_bonds then also with some error of linc wrning the
minimization is completed. When I do minimization without adding water
then there is no linc warning and minimization is completed but with
final positive potential energy. Then as suggested by Justin I used
smaller box and there also in simulated annealing stage the system
gives linc warning and the programme stops with fatal error. Please
tell me where I am wrong.
How about simplifying the problem. Does the system run under normal
conditions? In other words, can you run normal MD? You're treating the
system very harshly with the combination of high pressure and annealing.
Without seeing your .mdp file for this process, it's impossible to say
how
reasonable your settings are.
It is also possible that your parameters for CHAPS (if they are the
default
ones from PRODRG) are incorrect. The charges and charge groups nearly
always are. Without seeing them, there's nothing better to offer.
-Justin
shahid nayeem
On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham <mark.abra...@anu.edu.au>
wrote:
On 28/01/2011 3:51 PM, shahid nayeem wrote:
Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.
You've set up a system that isn't stable, but we don't have enough
information to have any idea why. "I tried with new box size" doesn't
go
close to describing your method in enough detail for anyone to know
where
you went wrong.
See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for
generic
tips
Mark
Please help.
shahid Nayeem
On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul<jalem...@vt.edu>
wrote:
shahid nayeem wrote:
Dear All
I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.
Original messge:
I am trying to prepare a solvation box of chaps. After generating
.itp
and .gro at ProDrg and thorough check of charges, I started with a
box
size of 6x6x6. Energy minimization, simulated annealing (Cooling
under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly. But finally I get a box where all water
molecules get accumulated in two three small region within the box
and
all chaps molecules gets accumulated in another small regions.I
wanted
near random uniform distribution of chaps in water. Any help from
user, where I am wrong and what should I do.
Reply to query.
I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
–ci 7 chaps.gro).Then I solvated the output box with genbox using
-maxsol 500 and spc216.gro. On visualization, at this stage itself
uniform solvation did not occur (I got water in one region and chaps
molecule in other region) but I observed a similar situation while
If your box was not completely solvated, then don't use -maxsol. A
box
of
6x6x6 nm should require more than 500 molecules of water to fill. If
you're
trying to achieve some specific mole fraction or concentration, then
re-figure your box size.
-Justin
preparing 10M urea salvation box. This was followed by 1ns simulated
annealing from temp 300K to 0K and pressure 100 bar, then 1ns
simulated annealing from temp. 0k to 300k and then ins
equilibriation
at this temperature. In case of urea finally I got uniformly
solvated
urea_water_box but in chaps I couldn’t get it.
Shahid Nayeem
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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