Hi,
have look here in the supp mat. of this paper:
http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/abstract
Mn2+ for OPLS ff in case you needed it
best
and
On 22/10/2014 16:13, Justin Lemkul wrote:
On 10/22/14 5:09 AM, yaser wrote:
hi
i tried add Mn in .itp file but its need
Hi Mark,
There was something in the matrix calculations that was not totally clear
to me. That is why I started to think in a different approach.
Now everything is fine.
Thank you very much,
Mario Fernández-Pendás
El 23/10/2014 01:15, Mark Abraham mark.j.abra...@gmail.com escribió:
Hi,
No,
Hi Doug,
I recently read a good review on ABF
http://pubs.acs.org/doi/abs/10.1021/jp506633n. It's focused on ABF but
there's a section which compares ABF to other techniques.
While I'm at it, are there any plans from gromacs devs to implement ABF
in gromacs?
Best,
Patrick
Le 20/10/2014
hi
Reading file md.tpr, VERSION 4.6.5 (single precision)
Using 4 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine,
which is better)
how can i use this features for better mdrun speed.
thanke you.
--
Gromacs Users mailing list
* Please search the archive at
Hi everyone.
I am new to Gromacs and have some question in the building part. I can only
genarate mdrun_mpi when set the DGMX_BUILD_MDRUN_ONLY to ON and when I
set it to OFF, it can only produce gmx_mpi and template in the bin
directory. What is the different between mdrun_mpi and gmx_mpi ?
Hello,
you need to recompile Gromacs with -DGMX_SIMD=AVX_256 flag. Or not set it and
cmake should detect and use the best version automatically.
http://www.gromacs.org/Documentation/Installation_Instructions_4.6
Cheers.
Milan
On Thursday 23 October 2014 13:32:31 Yaser Hosseini wrote:
hi
On 10/23/14 6:37 AM, Vinson Leung wrote:
Hi everyone.
I am new to Gromacs and have some question in the building part. I can only
genarate mdrun_mpi when set the DGMX_BUILD_MDRUN_ONLY to ON and when I
set it to OFF, it can only produce gmx_mpi and template in the bin
directory. What is the
On 10/23/14 1:47 AM, Kester Wong wrote:
Thanks for the input Mark,
Hi Mark,
Thanks for the input, I thought a time step of 2 fs is small enough?
Not always for unconstrained bonds. The largest stable time step is
determined by the size of the period of the
On 10/23/14 6:02 AM, Yaser Hosseini wrote:
hi
Reading file md.tpr, VERSION 4.6.5 (single precision)
Using 4 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine,
which is better)
how can i use this features for better mdrun speed.
The level of optimization
and how can I get those analysis tools?
On Thu, Oct 23, 2014 at 7:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/23/14 6:37 AM, Vinson Leung wrote:
Hi everyone.
I am new to Gromacs and have some question in the building part. I can
only
genarate mdrun_mpi when set the
On 10/23/14 7:48 AM, Vinson Leung wrote:
and how can I get those analysis tools?
http://www.gromacs.org/Documentation/Installation_Instructions
Everything gets built by default unless you use -DGMX_BUILD_MDRUN_ONLY=ON
-Justin
On Thu, Oct 23, 2014 at 7:31 PM, Justin Lemkul
On 10/23/14 8:03 AM, Vinson Leung wrote:
But I remove the option -DGMX_BUILD_MDRUN_ONLY=ON and can only get
gmx_mpi and template. There is no those analysis tools and my Gromacs
version is 5.0.2.
My build congfiure is like below:
Thanks. It seem to much more clear for me:).
I have compiled again with -DGMX_MPI=OFF. Now I have only two executable
file (gmx and template) in the bin dir. If I want to generate .xvg file
and I already have .edr file. What is the comand line exactly ?
Vincent
On Thu, Oct 23, 2014 at 8:05 PM,
On 10/23/14 8:26 AM, Vinson Leung wrote:
Thanks. It seem to much more clear for me:).
I have compiled again with -DGMX_MPI=OFF. Now I have only two executable
file (gmx and template) in the bin dir. If I want to generate .xvg file
and I already have .edr file. What is the comand line exactly
Thank you very much:) It help me a lot !
Best
Vincent
On Thu, Oct 23, 2014 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/23/14 8:26 AM, Vinson Leung wrote:
Thanks. It seem to much more clear for me:).
I have compiled again with -DGMX_MPI=OFF. Now I have only two executable
Dear gromacs user,
I would like to calculate Binding Free Energy Calculations for my
protein-DNA complex (already run for 50ns). Is there any manual or
tutorial (for more complex systems) available?
best regards
Urszula
-
Ta wiadomość została wysłana z
On 10/23/14 10:35 AM, Urszula Uciechowska wrote:
Dear gromacs user,
I would like to calculate Binding Free Energy Calculations for my
protein-DNA complex (already run for 50ns). Is there any manual or
tutorial (for more complex systems) available?
See published methods like g_mmpbsa (very
Dear Urszula,
Apologies for the self promotion, but we've made some attempts to do that for a
TF-DNA complex: http://www.pnas.org/content/110/49/19796. Note that the
rotational degrees of freedom are hard to sample and you may need some further
assumptions about mesoscopic scales for the
Hi,
thanks Justin to point out our tool GMXPBSA (GMXAPBS was the old one)
http://www.sciencedirect.com/science/article/pii/S0010465514002240
and new version 2.1:
http://www.sciencedirect.com/science/article/pii/S0010465514003154
The link to the program is still not avaliable but you can
Hello Gromacs users,
If I have all the files that were used to generate a trajectory file, what
is the proper procedure to update the atomnames in the trajectory. My best
guess is below. Is this problematic?
# remove first frame of trajectory
cat EOF tmp.ndx
[ FIRSTFRAME ]
1
EOF
trjconv -fr
On 10/23/14 4:29 PM, Eric Smoll wrote:
Hello Gromacs users,
If I have all the files that were used to generate a trajectory file, what
is the proper procedure to update the atomnames in the trajectory. My best
guess is below. Is this problematic?
# remove first frame of trajectory
cat EOF
Thanks for the guidance, Justin.
-Eric
On Thu, Oct 23, 2014 at 2:39 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/23/14 4:29 PM, Eric Smoll wrote:
Hello Gromacs users,
If I have all the files that were used to generate a trajectory file, what
is the proper procedure to update the
Dear gromacs users,
I try simulate protein folding using REMD sampling method in implicit
solvent. I run my simulation on MPI-compiled gromacs 5.0.2 on single node.
I have succesfully minimized equilibrated (NVT-constrained, and NPT
constrained) my system. However, In the middle of mdrun_mpi
Hi,
The warning message told you not to increase the table distance unless you
were sure the table distance was the problem. Why were you sure the table
distance was the problem, rather than some form of general instability of
your system? In addition to all the usual reasons for
Hi Justin and all,
Thanks for the input, I thought a time step of 2 fs is small enough?
Not always for unconstrained bonds. The largest stable time step is
determined by the size of the period of the fastest oscillation, which is
vibrations of bonds to
On 10/23/14 10:19 PM, Kester Wong wrote:
Hi Justin and all,
Thanks for the input, I thought a time step of 2 fs is small enough?
Not always for unconstrained bonds. The largest stable time step is
determined by the size of the period of the
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