Some respect for this user board would be nice.
If there is anything unclear about how gmx make_ndx works, please ask a
specific question instead of posting the same very unclear thing over
and over. Noone will be able to help with your question, because it
requires precise knowledge of your s
can anyone please give me some idea.
On 5/30/18, SHAHEE ISLAM wrote:
> hi,
> i want to calculate the contact between the backbone of protein(it is
> a coarse grained protein using martini force field).how i will make
> .ndx file to calculate the contact.
>
> thanking you
> shahee islam
> universi
hi,
i want to calculate the contact between the backbone of protein(it is
a coarse grained protein using martini force field).how i will make
.ndx file to calculate the contact.
thanking you
shahee islam
university of calcutta
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My bad, I missed a line in the warning message:
Building NVCC (Device) object
src/gromac/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj
CMake Warning (dev) at
libgromacs_generated_nbnxn_cuda.cu.obj.Release.cmake:74:
Syntax Warning in cmake code a
Dear Micholas,
I have many hydrocarbons (small to large) for study, C8 - C50, .
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Hi,
I've implemented the fix and I verified that it works on the command line; I've
successfully complied the nvcc depend file.
Nonetheless, CMake still fails on compiling in that stage. Here is the error
message in Visual studio 2015
CMake Error at libgromacs_generated_nbnxn_cuda.cu.obj.Rele
Since octane is not huge hydrocarbon, you could use LigParGen (
http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html ) from Jorgensen's lab
to generate an itp file for octane, which you could use as your guide to build
an rtp.
-Micholas
===
Micholas Dean Smith, PhD. MRSC
Post
On 5/29/18 3:11 PM, Nagasree Garapati wrote:
Dear all
I am getting following error while running NPT simulation.
I did energy minimization and NVT simulations, which ran successfully but when
I proceed to NPT simulation, I am getting below error.
Step 142, time 0.284 (ps) LINCS WARNING
On 5/29/18 3:08 PM, mostafa paknia wrote:
Hi
I have two topology files already
One of them is CNT's topology & otherone is a drug topology
I want to make them just one
How can i do that
I already answered this a few days ago:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018
Dear all
I am getting following error while running NPT simulation.
I did energy minimization and NVT simulations, which ran successfully but when
I proceed to NPT simulation, I am getting below error.
Step 142, time 0.284 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms -na
On 5/29/18 3:08 PM, Atila Petrosian wrote:
I know your mean. But there is not octane residue type in rtp file.
Then you'll have to make one, using the existing molecules as a guide.
The OPLS atom types for such a species should be straightforward to assign.
-Justin
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Hi
I have two topology files already
One of them is CNT's topology & otherone is a drug topology
I want to make them just one
How can i do that
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I know your mean. But there is not octane residue type in rtp file.
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On 5/29/18 2:50 PM, Atila Petrosian wrote:
I did what was in README for octane molecule, but:
Fatal error:
Residue 'LIG' not found in residue topology database.
Your input coordinates use a generic name (that most model-building
programs use) that pdb2gmx doesn't recognize. Rename appropri
I did what was in README for octane molecule, but:
Fatal error:
Residue 'LIG' not found in residue topology database.
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On 5/29/18 2:43 PM, Atila Petrosian wrote:
Dear Justin,
I found L-OPLS in GitHub:
https://github.com/wesbarnett/lopls
Can I use it directly for hydrocarbon such as octane?
I have no experience with those parameters. Test them and make sure they
reproduce what's in the paper.
-Justin
-
Dear Justin,
I found L-OPLS in GitHub:
https://github.com/wesbarnett/lopls
Can I use it directly for hydrocarbon such as octane?
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On 5/29/18 2:30 PM, Atila Petrosian wrote:
Hi,
I found a paper entitled " Optimization of the OPLS-AA Force Field for Long
Hydrocarbons " (https://pubs.acs.org/doi/abs/10.1021/ct200908r). They
obtained L-OPLS force field.
Which version of gromacs has L-OPLS force field?
None, you'll have t
Hi,
I found a paper entitled " Optimization of the OPLS-AA Force Field for Long
Hydrocarbons " (https://pubs.acs.org/doi/abs/10.1021/ct200908r). They
obtained L-OPLS force field.
Which version of gromacs has L-OPLS force field?
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Thanks Justin.
On Tue, May 29, 2018 at 11:09 AM, Justin Lemkul wrote:
>
>
> On 5/29/18 12:04 PM, Lakshman Ji Verma wrote:
>
>> Thanks Justin. A follow up question for my better understanding.
>>
>> Does it mean that with “periodic-molecules” False, the periodic images
>> won’t affect interaction
On 5/29/18 12:04 PM, Lakshman Ji Verma wrote:
Thanks Justin. A follow up question for my better understanding.
Does it mean that with “periodic-molecules” False, the periodic images
won’t affect interactions in the actual simulation box, whereas they will
affect if I keep “periodic-molecules”
Thanks Justin. A follow up question for my better understanding.
Does it mean that with “periodic-molecules” False, the periodic images
won’t affect interactions in the actual simulation box, whereas they will
affect if I keep “periodic-molecules” True?
Thanks
Lakshman
On Tue, May 29, 2018 at 10
On 5/29/18 11:50 AM, Lakshman Ji Verma wrote:
What difference it will make I keep Periodic molecules option True or False?
I read the manual but couldn’t understand more than keeping it False will
be faster.
The "periodic-molecules" option is for use with "infinite" systems like
CNT, surface
What difference it will make I keep Periodic molecules option True or False?
I read the manual but couldn’t understand more than keeping it False will
be faster.
Thanks!
Lakshman
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Hi,
Sure, that's what trjconv -pbc and -ur are used for. There's no way to ask
mdrun to automatically do the particular operation you want.
Mark
On Tue, May 29, 2018 at 3:21 PM Alex wrote:
> Hi Mark,
> Thanks.
> The problem is that only the slab shifts and water molecules stay x-y
> centrally
Hi Mark,
Thanks.
The problem is that only the slab shifts and water molecules stay x-y
centrally in the box. Similar to the picture in the link below:
https://drive.google.com/open?id=1TwkgpesJPfFUiqxhl9rXBU33dwWn-tyD
Regards,
Alex
On Fri, May 25, 2018 at 5:30 AM, Mark Abraham
wrote:
> Hi,
>
> m
Hi,
i am trying to parametrize a Metal-Organic-Framework for later gromacs
simulations. Does anybody have experience in deriving parameters like
force constants completely from theory? I know that there are techniques
doing it with DFT-calculations but i would like to know other methods as
we
i have followed this tutorial
http://cgmartini.nl/index.php/tutorials-general-introduction/proteins
On 5/29/18, SHAHEE ISLAM wrote:
> hi,
> i want to calculate the contact between the backbone of protein(it is
> a coarse grained protein using martini force field).how i will make
> .ndx file to ca
hi,
i want to calculate the contact between the backbone of protein(it is
a coarse grained protein using martini force field).how i will make
.ndx file to calculate the contact.
thanking you
shahee islam
university of calcutta
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