shikha agarwal wrote:
hi,
HAPPY NEW YEAR
I am experiencing a segmentation fault during mdrun in equlibration step .
error
Wrote pdb files with previous and current coordinates
[shikha-desktop:01719] *** Process received signal ***
[shikha-desktop:01719] Signal: Segmentation fault (11)
[shikha
Dear All
In doing umbrella sampling ,when I want to generate NPT every thing is
going well but one error is occuring in the first.
please let me know how can I solve this problem.
Is it usefull to extend the degree which is defined in .mdp file?
Step 0, time 0 (ps) LINCS WARNING
relative constrai
mohsen ramezanpour wrote:
Dear All
In doing umbrella sampling ,when I want to generate NPT every thing is
going well but one error is occuring in the first.
please let me know how can I solve this problem.
Is it usefull to extend the degree which is defined in .mdp file?
No. The constraints
On 2/01/2011 2:18 PM, sreelakshmi ramesh wrote:
Dear all,
I have a protein in water and i have simulated it for few
nanoseconds and i now i wanted to monitor the The sum of the O-H
distances (in Å) of the backbone
hydrogen bonds ROH:i dono how to extract the value from the traject
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On 1/3/11, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>> Dear All
>> In doing umbrella sampling ,when I want to generate NPT every thing is
>> going well but one error is occuring in the first.
>> please let me know how can I solve this problem.
>> Is it usefull to extend the degree
mohsen ramezanpour wrote:
On 1/3/11, Justin A. Lemkul wrote:
mohsen ramezanpour wrote:
Dear All
In doing umbrella sampling ,when I want to generate NPT every thing is
going well but one error is occuring in the first.
please let me know how can I solve this problem.
Is it usefull to extend
Dear Justin and Chris
very thanks for your reply and guidance.
I did all the steps successfully. then I used (./my_tool -f final.xtc -o
final.pdb -b 300 -e 350), the final.pdb file was created without problem.
when I opened final.pdb file by text editor, order of waters and ions in
final.pdb was
for example ordering in final.pdb is as follows:
ATOM 1856 N2 DG3 X 86 15.620 47.770 21.660 1.00
0.00
ATOM 1857 H21 DG3 X 86 16.480 48.290 21.560 1.00
0.00
ATOM 1858 H22 DG3 X 86 15.010 48.060 22.420 1.00
0.00
ATOM 1859 N3 DG3 X 86 14.160 46.250 20.
Dear all,
Firstly, I wish you a happy new year filled with joy, health and lots of
finding !!
Now my question:
I have simulated one peptide (25 AA length + N- and C- caps) in two
environment: one in bulk water TIP3P water (A) and one with a DPC micelle in
water (B). My peptide keep in the
sa wrote:
Dear all,
Firstly, I wish you a happy new year filled with joy, health and lots of
finding !!
Now my question:
I have simulated one peptide (25 AA length + N- and C- caps) in two
environment: one in bulk water TIP3P water (A) and one with a DPC
micelle in water (B). My pepti
Hey Leila,
Why all the fuzz? You can do this with trjconv using an index file.
The following oneliner (:$) should write you the index file you need.
python -c
'r,a,b,c=range,1868,24086,24100;open("r.ndx","w").write("[x]\n"+"\n".join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'
Hope it helps,
Tsj
Hi all
I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
107.40, 112.20) and Isotropic pressure coupling. Now i want to use
average box size for production run (NVT). But I am confused because i
am not able to get the meaning of the output values of the log file.
Log file output
Hi Navjeet,
The box is defined as a triangular matrix, so the volume equals the product
of the diagonal elements.
Hope it helps,
Tsjerk
On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat" wrote:
Hi all
I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
107.40, 112.20) and Isotropic pr
Dear Tsjerk
thanks for your reply
I have not experience in using python.
in [python -c
'r,a,b,c=range,1868,24086,24100;open("r.ndx","w").write("[x]\n"+"\n".join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'].
r.ndx contains all the atoms. is it true?
why did you use r,a,b,c=range,1868,24086,24100
It seems like Tsjerk has a better solution. It appears that you need
only to have an index group in which the atoms are ordered in the
output order that you desire. Therefore, if you wanted to reverse the
order of the first 3 atoms, you would create an index file like this:
[ my_group ]
3 2
Hi Leila,
r.ndx would be the index file indeed. Sorry for not explicitly mentioning
that. For the rest, the most important question is 'did it work?' Knowing
python is not so important, unless you're determined to understand how it
works :) As for the numbers, python always goes up to, not includi
Hi everybody,
I am starting to simulate ethanol-trifluoroethanol mixtures with opls
aa, but TFE is not defined in the opls rtp file, so I added a new entry.
I would like to confirm if the way the charge groups are defined for
ethanol are mantained for TFE:
CB 1
HB11
HB21
HB3
On 4/01/2011 9:39 AM, Marcelo Silva wrote:
Hi everybody,
I am starting to simulate ethanol-trifluoroethanol mixtures with opls
aa, but TFE is not defined in the opls rtp file, so I added a new
entry. I would like to confirm if the way the charge groups are
defined for ethanol are mantained fo
Dear Email Sender,
Thank you very much for contacting me! Unfortunately, I am not available in the
office at the moment and cannot respond to your email. I will be able to handle
your request starting again Monday, January 10, 2011.
For all questions about CloudBroker, please contact the compan
On 4/01/2011 11:23 AM, wibke.sudh...@cloudbroker.com wrote:
Dear Email Sender,
Thank you very much for contacting me! Unfortunately, I am not available in the
office at the moment and cannot respond to your email. I will be able to handle
your request starting again Monday, January 10, 2011.
Hi Gromacs users,
I used g_mindist to calculate the minimum distance between a residue and
a group of water molecules.
Since distance is a length between two points in space, for the program
considers the bunch of water molecules(15 number)
what specific point does the group consider ? Thank yo
Ramachandran G wrote:
Hi Gromacs users,
I used g_mindist to calculate the minimum distance between a residue
and a group of water molecules.
Since distance is a length between two points in space, for the program
considers the bunch of water molecules(15 number)
what specific point does
Thanks a lot for your reply..
On Mon, Jan 3, 2011 at 6:07 PM, Mark Abraham wrote:
> On 2/01/2011 2:18 PM, sreelakshmi ramesh wrote:
>
>> Dear all,
>> I have a protein in water and i have simulated it for few
>> nanoseconds and i now i wanted to monitor the The sum of the O-H distance
Hi expert,
I'd like to add sufactant to water. That means i should first get the
sufactant.gro, and sufactant.top.
Someone said that we cannot get sufactant.gro and sufactant.top through grompp
() sufactant.pdb. Because grompp .pdb could mainly use for macro-biology big
moleculars, which m
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