Others have asked for this functionality before and it would make sense to
implement it. However, no one is working on that at the moment and I suspect no
one will on the short term since the analysis framework will be overhauled
eventually. For now, you can use g_hbond -contact, which allows
Thanks a ton, Erik. I have looked in similar questions and found similar
answers to use -contact option. But it did not help. Neither for me nor for the
one who has asked the question earlier.
I am trying the following command
g_hbond -f md_2ns_nopbc.xtc -s md_2ns.tpr -num hbCl-Urea.xvg
Strange. Could you send the tpr and a short xtc for me to play with?
Erik Marklund, PhD
Postdoctoral Research Associate
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 10 Feb 2014, at 10:11, Dhawal Shah
Dear Sir,
I have question w.r.t gromacs-4.6.4 installation with GPU support.
I have installed non-GPU vesion(for 4.6.4) and it works fine.
But while compiling with gpu (-DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/opt/CUDA-5.5)
It gives compilation error. The node is having gpu card fermi and cuda5.5.
On Mon, Feb 10, 2014 at 1:27 PM, Chaitali Chandratre
chaitujo...@gmail.com wrote:
Dear Sir,
I have question w.r.t gromacs-4.6.4 installation with GPU support.
I have installed non-GPU vesion(for 4.6.4) and it works fine.
But while compiling with gpu (-DGMX_GPU=ON
Dear All
I am planning to study the effect of adding the ions on the dodecamer
protein.
For this purpose I need to add ions (Fe2+) in the system. Any suggestion
for it. I have come to know through various discussion forums that there
is no need of adding ions to make the system neutral, but in
Hi Dhawal,
One way you can try is to manually change ｔｈｅ name of chloride to oxygen so
that the g_hbond code can treat the new atom name as acceptors. Just modify
.gro file, .top file and ions.itp file and get a new tpr file. And use the
rerun option of mdrun to get a new trajectory. Then you
On 2/10/14, 9:52 AM, Jianguo Li wrote:
Hi Dhawal,
One way you can try is to manually change ｔｈｅ name of chloride to oxygen so
that the g_hbond code can treat the new atom name as acceptors. Just modify
.gro file, .top file and ions.itp file and get a new tpr file. And use the
rerun option
On 2/10/14, 7:47 AM, prasun kumar wrote:
Dear All
I am planning to study the effect of adding the ions on the dodecamer
protein.
For this purpose I need to add ions (Fe2+) in the system. Any suggestion
for it. I have come to know through various discussion forums that there
is no need of
Dear Justin
Sending you the personal email for thanking you for the quick reply and the
tutorials you have put on your website (especially Umbrella sampling)
Thanx alot.
PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success
On Mon, Feb 10, 2014 at 8:34 PM, Justin
Dear All and Justin
Thanx for the quick reply...
My aim is to find the effect of the ion on the dodecamer (whether on adding
ions it is stable or not)
Seeing the system.. I am left with two options (My view): 1) Coarse Grain
Method or 2. Implicit Solvent Method
Coarse Grain Method is full of
Hello,
I am trying to perform peptide simulation using TFE-water system. I did lot
of literature search and according carried out NVT for 32ns followed by NPT
10ns simulation for TFE-water system.
I found that the TFE get accumulated in the center of the box and water
molecules surround them.
On 2/10/14, 11:31 AM, prasun kumar wrote:
Dear All and Justin
Thanx for the quick reply...
My aim is to find the effect of the ion on the dodecamer (whether on adding ions
it is stable or not)
Seeing the system.. I am left with two options (My view): 1) Coarse Grain Method
or 2. Implicit
On 2/10/14, 12:12 PM, Archana Sonawani-Jagtap wrote:
Hello,
I am trying to perform peptide simulation using TFE-water system. I did lot
of literature search and according carried out NVT for 32ns followed by NPT
10ns simulation for TFE-water system.
I found that the TFE get accumulated in
Hello again Archana,
Glad to see you managed to build the system and simulate it since we last
exchanged e-mails.
In my simulations TFE is never 100% miscible but doesn't also display such
hydrophobic behavior as you report here. However it's hard to answer your
questions without more
Now I successfully ( I believed so) incorporated both protonated and
deprotonated states of GLU residue in the .top file. As I am trying to
energy minimize the system, it gives me an error saying:
WARNING 1 [file GLUTest3_GROMOS_p.top, line 52]:
Some parameters for bonded interaction involving
Do you have a suggestion how can I solve it Justin?
--
View this message in context:
http://gromacs.5086.x6.nabble.com/free-energy-calculations-for-reference-state-for-constant-pH-MD-simulations-tp5014084p5014447.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
On 2/10/14, 3:57 PM, Mehmet Ozbil wrote:
Do you have a suggestion how can I solve it Justin?
The error message tells you exactly what the offending line is for the bonded
interaction and you can easily check your math with regards to the charge.
Without seeing the entire topology, I can
On 2/10/14, 3:59 PM, shivangi nangia wrote:
Dear Gromacs users,
I have a question regarding the input file group.dat that has to be
supplied for using g_enemat.
The manual says With *-groups* a file must be supplied with on each line a
group to be used.
I need to calculate the interaction
Yes the error message indicates about the line which is in the very end ( 6 7
2 gb_27). I can see which atoms they are, 6 and 7, but I don`t know how to
solve it??? My part of top file is below, with the line it is complaining about
in bold. Thank you very much.
Include forcefield
Dear Sir,
Below is error message for gromacs-4.6.4 gpu enabled install:
---
make error :
[chaitalij@gpu4 build-gpu]$ make
[ 0%] Building NVCC (Device) object
Hello everyone,
I have done a set of molecular dynamic simulation of my protein and its
mutated structure, now please tell me how should I validate the
simulation results or structures. Whether I can reproduce the same
simulations.
Thank you in advance
--
Ananya Chatterjee,
Senior Research
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