On 08/22/2012 08:23 AM, Mark Abraham wrote:
The authors use a 200x200 grid in their first published work with this
tool. What makes you think 20 is enough? (And even if it is enough,
you still haven't demonstrated another calculation showing that the
APL with the embedded protein should be diff
Hello,
I'm new in Gromacs. I'm using gromacs 4.5.3. I need help with pdb format. I use
to convert my file by PRODRG and MN.CONVERT.
I'm trying to create a topology file from the pdb using the pdb2gmx. I get an
error.
My molecules are quaternary ammonium salts.
My pdb file by MN. CONVERT:
HEADER
On 8/22/12 7:44 AM, Sylwia Chmielewska wrote:
Hello,
I'm new in Gromacs. I'm using gromacs 4.5.3. I need help with pdb format. I use
to convert my file by PRODRG and MN.CONVERT.
I'm trying to create a topology file from the pdb using the pdb2gmx. I get an
error.
My molecules are quaternary a
On 8/22/12 3:16 AM, Albert wrote:
On 08/22/2012 08:23 AM, Mark Abraham wrote:
The authors use a 200x200 grid in their first published work with this tool.
What makes you think 20 is enough? (And even if it is enough, you still
haven't demonstrated another calculation showing that the APL with
Hi,
I am trying to run NPT equilibration on two separate systems both with
ligands present in the structure.
However, I got two different errors for both of these and these are below:
Fatal error: A charge group moved too far between two domain
decomposition steps.
Fatal error: 8 particles comm
On 8/22/12 8:26 AM, Ankita naithani wrote:
Hi,
I am trying to run NPT equilibration on two separate systems both with
ligands present in the structure.
However, I got two different errors for both of these and these are below:
Fatal error: A charge group moved too far between two domain
deco
Thank you for your prompt reply. I will take to read about force field.
Could you recommend websites for field force? Or other information about force
field.
Best Regards
Sylwia
- Oryginalna wiadomość -
Od: "Justin Lemkul"
Do: "Discussion list for GROMACS users"
Wysłane: środa, 22 sierp
On 8/22/12 8:48 AM, Sylwia Chmielewska wrote:
Thank you for your prompt reply. I will take to read about force field.
Could you recommend websites for field force? Or other information about force
field.
You can find primary literature for the various force fields available in
Gromacs with
Thanks.
Sylwia
- Oryginalna wiadomość -
Od: "Justin Lemkul"
Do: "Discussion list for GROMACS users"
Wysłane: środa, 22 sierpień 2012 14:56:16
Temat: Re: [gmx-users] pdb file error
On 8/22/12 8:48 AM, Sylwia Chmielewska wrote:
> Thank you for your prompt reply. I will take to read abou
hello Justin:
thanks for reply.
I've read both the paper and manual script. As indicated from the
output, I found the following line:
3684.2953.8840018217
I just wondering how could it possible fro residue 368 with a value of 3.88?
For the pure lipids/water case, my apology for thi
On 8/22/12 9:12 AM, Albert wrote:
hello Justin:
thanks for reply.
I've read both the paper and manual script. As indicated from the output, I
found the following line:
3684.2953.8840018217
I just wondering how could it possible fro residue 368 with a value of 3.88?
My guess wo
hello Justin:
thanks for reply.
I've checked this residue, it is close to protein but I am still
curious for the value with 3.88. Even we also observe something 11, 13
which are the same weired to me. here is the screen shot for this residue.
https://dl.dropbox.com/u/56271062/1.jpg
thanks
On 8/22/12 9:54 AM, Albert wrote:
hello Justin:
thanks for reply.
I've checked this residue, it is close to protein but I am still curious for
the value with 3.88. Even we also observe something 11, 13 which are the same
weired to me. here is the screen shot for this residue.
https://dl.
Hi justin,
Thanks for the suggestion. I will look at the code. Meanwhile I have
one doubt regarding the following option of the g_msd tool.
“-trestarttime 10 Time between restarting points in trajectory (ps)”
What does this -trestart indicates actually. I did a small trail run
on a 100p
On 8/22/12 12:12 PM, Bala subramanian wrote:
Hi justin,
Thanks for the suggestion. I will look at the code. Meanwhile I have
one doubt regarding the following option of the g_msd tool.
“-trestarttime 10 Time between restarting points in trajectory (ps)”
What does this -trestart indi
Dear All,
I am trying to install Gromacs 4.6 with -DGMX_OPENMM=ON
I am getting the following errors in make install-mdrun
../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_thread_num'
../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_num_threads'
../mdlib/libmd_openmm.so.6: u
On 08/22/2012 03:58 PM, Justin Lemkul wrote:
On 8/22/12 9:54 AM, Albert wrote:
hello Justin:
thanks for reply.
I've checked this residue, it is close to protein but I am still
curious for
the value with 3.88. Even we also observe something 11, 13 which are
the same
weired to me. here
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