@ Justin,
Thanks. I fixed the index files like you suggested. I’m getting logical results
now.
All the best,
On Nov 2, 2013, at 7:11 PM, Justin Lemkul wrote:
>
>
> On 11/2/13 7:01 PM, Xu Dong Huang wrote:
>> Should I perhaps make an edit in the index file for group 1 t
Should I perhaps make an edit in the index file for group 1 to be particle 1
and 2, and group 2 = particle 2 and 3?
On Nov 2, 2013, at 6:50 PM, Xu Dong Huang wrote:
> @ Gromacs users,
>
> so I did g_dist , and I’m confused by a couple of things. 1) why is it asking
> me for
260.0000.0000.0000.0000.000
…
Thanks in advance,
Xu Huang
On Nov 2, 2013, at 6:35 PM, Justin Lemkul wrote:
>
>
> On 11/2/13 6:29 PM, Xu Dong Huang wrote:
>> Dear All,
>>
>> My martini system has 3 particles in a chain, res
Dear All,
My martini system has 3 particles in a chain, rest is martini water, and I’m
only interested in the bond length distribution of particle 1&2, 1&3 and 2&3,
and I execute the following:
g_bond -f npt.xtc -n index.ndx -o bonds.xvg
I get the following error:
Total number of samples
Dear all,
I would like to assess the probability distribution of particle bond
distance/length over the entire run, specifically I want to collect possibly a
histogram representation or even a regular plot. Would using g_bond be the
correct way to obtain the probability distribution? Or is ther
wrote:
>
>
> On 10/31/13 4:44 PM, Xu Dong Huang wrote:
>> @ Justin,
>>
>> I did not define [angles] in the topology but I do have the angles result
>> from All-atom run using OPLS forcefield. The reason for me not to include it
>> in MARTINI forcefield to
e 3 particle display an angle similar to traditional
run.
On Oct 31, 2013, at 4:26 PM, Justin Lemkul wrote:
>
>
> On 10/31/13 4:22 PM, Xu Dong Huang wrote:
>> @ Justin,
>>
>> That doesn’t sound very good. I tried it as he suggested using make_ndx, it
>> seems
@ Justin,
That doesn’t sound very good. I tried it as he suggested using make_ndx, it
seems to work, but it’s not reporting the result I want. When I use g_angle
using the index i created, I chose the group I want to assess (My compound is
very simple in Martini, it’s only represented by 3 atom
31, 2013, at 1:38 PM, Justin Lemkul wrote:
>
>
> On 10/31/13 1:36 PM, Xu Dong Huang wrote:
>> Dear all.
>>
>> Since I am interested in finding the average angle, dihedrals in my system,
>> I attempted to use g_angle, but then I realized I need to make index f
Dear all.
Since I am interested in finding the average angle, dihedrals in my system, I
attempted to use g_angle, but then I realized I need to make index file using
mk_angndx,
I issued the following:
mk_angndx -s npt.tpr -n angle.ndx
and then i used g_angle -f not.xtc -n angle.ndx -ov angle.x
Hello,
I have couple objectives as part of an analysis of my simulated system. And I
would like some opinions on the tools to use to achieve it.
I have the following interest in my system:
1) Find the probability distribution (density) of bond angle on my molecule
between (i.e atom 12, 2,3 , 1
Dear gromacs users,
I just realized that even after trying to re-start a run, i still got separate
name files (idk why), but I managed to combine err, xtc files, but don't know
how to bring 2 .cpt files together, or is it not required? I'm trying to do NPT
run next, and it will -t *.cpt, but I
I see,
Thank you for the information Justin.
On Sep 28, 2013, at 2:57 PM, Justin Lemkul wrote:
>
>
> On 9/28/13 2:52 PM, Xu Dong Huang wrote:
>> Justin,
>>
>> I see. Is there a way to *stitch* the two files together so I can continue
>> onto a NPT run?
Justin,
I see. Is there a way to *stitch* the two files together so I can continue onto
a NPT run?
On Sep 28, 2013, at 2:49 PM, Justin Lemkul wrote:
>
>
> On 9/28/13 2:46 PM, Xu Dong Huang wrote:
>> Hello gromacs users,
>>
>> I restarted my run due to powe
Hello gromacs users,
I restarted my run due to power failure using mdrun -v -s .tpr -cpi
.cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make
it so it continues to update the original .xtc and .tpr files?
Thanks,
Xu Huang
Research Assistant
Chemical & Biochemica
Preeti,
if do_dssp doesn't work for you, try to do it manually using the following web
service:
http://www.cmbi.ru.nl/hsspsoap/
I use it because my platform (MAC OSX) can't run DO_DSSP
Best of luck!
On May 14, 2013, at 11:00 AM, Preeti Choudhary
wrote:
> I am facing problem while using do
If I don't specify -extend (time) , will it automatically use the time step
defined in the .tpr i'm using?
Or should I just define the time anyway ?
Thanks
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 27, 2013,
Thank you. I was just reading that as well, but didn't realize it could also be
used to extend. I thought it was just runs that terminated early.
Thanks
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 27, 2013, at 9:51 P
Dear advanced users,
I'm trying determine the procedure for extending NPT run (i.e I realized the
NPT run I did wasn't long enough, so I wish to run it for another million
steps. ) what should I do to set up the run again continuing with the previous
data?
Thanks,
Xu Dong Huan
@ Justin,
Thank you, that worked like a charm! (Using increased vanderwal distance)
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 8:42 PM, Xu Dong Huang wrote:
> Everytime I remove the atom that is causing
inly not overlapping with
my solute. )
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 8:12 PM, Xu Dong Huang wrote:
> Dear users,
>
> Now I fixed the initial structure error, and I solvated it in water (
= 0.9
rvdw = 1.2
My system size 73191 W, and 1 star (consisted of 101 atoms)
I read somewhere that it's that atom 14524 is overlapping… I can't visually see
anything complicated in my VMD since the system is pretty big
Xu Dong Huang
Chemical & Biochemical
Must be something wrong with my editor program (BBEdit), because when I open
the file you sent me, it shows me there an additional blank line. Ok, time to
switch to regular text editor…
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers
Oh, you have an Additional line after vector size box…. I thought you said to
remove that blank line
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:58 PM, Xu Dong Huang wrote:
> @Justin,
>
> I did
@Justin,
I did that, and it still says I have 103.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:49 PM, Xu Dong Huang wrote:
> @Justin,
>
> I did what you suggested, and I still can't load
@Justin,
I did what you suggested, and I still can't load my molecule in VMD. Maybe I am
still doing something wrong with the new line character thing.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:
@ Justin,
I laughed. :) Thank you. I can't believe I miss the smallest and most
rudimentary things.
Thanks again,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:20 PM, Justin Lemkul wrote:
>
>
&
@ Justin,
Thanks for always saving me from my mistakes. But I don't quite understand what
is a new line character?
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:12 PM, Justin Lemkul wrote:
>
>
//docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg
Thanks for any input.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Pleas
@ Justin,
Thank you.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 5, 2013, at 9:15 PM, Justin Lemkul wrote:
>
>
> On 1/5/13 9:08 PM, Xu Dong Huang wrote:
>> Dear gromac users,
>>
>> If I wi
Dear gromac users,
If I wish to measure the distance from 1 end of my polymer to the other end,
would it be valid to use g_gyrate? Even so, does that report just the radius,
hence the function name radius of gyration?
Thanks,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers Schoo
@Justin,
Yeah I allowed the NVT to run for way too long. Therefore I get a super clumped
structure. (Where as I only wanted a slightly clumped structure). I reduced the
nsteps to about 3000 from 100 thousand to achieve my desired structure.
Thanks for the support.
Xu Dong Huang
Chemical
d see if I get a less
clumped structure.
Thank you Justin, and sorry for the impulsive question.
I'll let you know if there is a further problem.
Thanks,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 5, 2013, at 8:
e it's too long and my message will be
held for approval by gmx)
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 5, 2013, at 8:31 PM, Justin Lemkul wrote:
>
>
> On 1/5/13 8:29 PM, Xu Dong Huang wrote:
>&
direction, no
beads are in bond connection as they should be. Any insight into why my polymer
blew up in vacuum? (please let me know what kind of additional information
you'd like to see)
Thanks,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineer
The average of all my variations contain about 802780 atoms.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 3, 2013, at 9:36 PM, Justin Lemkul wrote:
>
>
> On 1/3/13 9:33 PM, Xu Dong Huang wrote:
>>
Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45
box system with water solvent + large multiple solutes.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 3, 2013, at 9:29 PM, Xu Don
run of that size? Or am I just faced with slow
technology. Or am I doing something wrong (I requested 6 cores for my run)
Please let me know, thanks.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
--
gmx-users mailing listgmx-u
just martini defined water system.
The first 50 beads of all 4 arms has hydrophobic interaction with the Water
solvent. and the last 5 remaining beads on all 4 arms are set to have extreme
similar hydrophilic interaction with martini water bead.
Xu Dong Huang
Chemical & Biochemical Enginee
@Justin,
forgot to mention, yes the NVT was ran using MPI as well. (You're right, the
MPI is not the issue, because I took the file off my cluster and attempted to
run NPT on my personal computer, it reported same segmentation error, fault 11)
Xu Dong Huang
Chemical & Biochemical En
95e-027.05573e+02 -4.79105e-03
-2.47909e-01 -4.78920e-037.07047e+02
Total Dipole (D)
0.0e+000.0e+00 0.00000e+00
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 2, 2013, at 3:20 PM, Xu Dong
ing
xudo...@eden.rutgers.edu
On Jan 2, 2013, at 3:08 PM, Xu Dong Huang wrote:
> Dear gromac users,
>
> after running a successful NVT, I was going to run NPT. (All ran with MPI),
> however when I attempt to run the NPT, I get the following segmentation
> error:
>
> Getting Lo
deffnm npt
-Is my system blowing up? Or there is something wrong with MPI ? (I
requested 4 processors)
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailma
@Justin,
Does the philosophy described in your tutorial apply to CG martini bead models
where 1 bead describes the entire CO2 atom? (If I were to do that, assuming)
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 1, 2013, a
Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 1, 2013, at 10:38 PM, Justin Lemkul wrote:
>
>
> On 1/1/13 10:33 PM, Xu Dong Huang wrote:
>> Dear advanced gromac users,
>>
>> I am trying to simulate a lon
/Documentation/Errors
Please let me know if there is a way to go around that. Thank you.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-u
Thank you very much. I got it sorted out by following your advice.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Dec 31, 2012, at 10:23 PM, Justin Lemkul wrote:
>
>
> On 12/31/12 9:41 PM, Xu Dong Huang wrote:
>
t of the box)
-How can I prevent that from happening? So that I can put as many additional
polymer in the solvated system as I want?
Thanks,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
--
gmx-users mailing listgmx-
Ok I sent it.
Let me know if you did not receive them.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Dec 31, 2012, at 5:54 PM, Justin Lemkul wrote:
>
>
> On 12/31/12 5:50 PM, Xu Dong Huang wrote:
>> Dear
ays:
Read 201 atoms …blah blah blah.. , as it should I'm assuming if the .gro is
valid?
Please let me know, thank you.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Dec 31, 2012, at 5:40 PM, Xu Dong Huang wrote:
> D
*Even though according to the .gro coordinates, those beads of 175 and up are
jumped, i don't see the relocated beads anyhow in this VMD viewing. I'm so
confused of what is happening.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.ru
2star O2 183 12.421 26.181 16.695
Notice the jump on atom number 174 and 175, why is there a sudden coordinate
jump?
All i can see in VMD is my negative axis part of the molecule beads are cut
off.
Any input is appreciated. Thank you!
Xu Dong Huang
Chemical & Biochemical Enginee
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