Sir,
I want to calculate MSD within a cutoff range, how can I wrote a command
for that. Can you help me regarding this?
Thank you
On Wed, Aug 28, 2019, 11:15 Mark Abraham wrote:
> Hi,
>
> There's lots of documentation and examples available. See
>
> http://manual.gromacs.org/documentation/curren
Hi,
There's lots of documentation and examples available. See
http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#selection-syntax-and-usage
Mark
On Wed, 28 Aug 2019 at 07:14, Omkar Singh wrote:
> Hi everyone
> Can anyone help me regarding "gmx select" command making a inde
Hi everyone
Can anyone help me regarding "gmx select" command making a index file
within a cutoff.
Thanks
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Dear Dr. Dallas Warren
Thanks a lot
Maryam
On 2019-05-27 02:09, Dallas Warren wrote:
> "|" = or
>
> What you want is "&" = and
>
> aptamer | r special = aptamer
> aptamer & r special = special
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institut
"|" = or
What you want is "&" = and
aptamer | r special = aptamer
aptamer & r special = special
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
--
Dear all, I am going to generate index file for special residues in my
aptamer, I use the command " make_ndx -f *.gro -o index.ndx and then
select group as DNA and Special residue as fallow ">1|r 4 5 7 36.
The index file for whole aptamer and special residue is similar, I would
be appreciate an
You need to combine the C-alpha default group with the selected category
with the & operator.
On Mon, May 7, 2018 at 3:31 PM RAHUL SURESH wrote:
> Hi, I have created the index file. Now I want to calculate the rmsd of the
> C-alpha atoms of the index group alone.. So what group should i select?
On 5/7/18 9:31 AM, RAHUL SURESH wrote:
Hi, I have created the index file. Now I want to calculate the rmsd of the
C-alpha atoms of the index group alone.. So what group should i select?
Please state your goals directly rather than leaving details to come out
bit by bit, it's much more effici
Hi, I have created the index file. Now I want to calculate the rmsd of the
C-alpha atoms of the index group alone.. So what group should i select?
On Mon, May 7, 2018 at 6:50 PM, RAHUL SURESH
wrote:
> thank you.
>
> On Mon, May 7, 2018 at 3:39 PM, Shreyas Kaptan
> wrote:
>
>> It's 'r37-70 | r 1
thank you.
On Mon, May 7, 2018 at 3:39 PM, Shreyas Kaptan
wrote:
> It's 'r37-70 | r 120-167 | ...' so on and so forth.
>
> On Mon, May 7, 2018 at 12:06 PM RAHUL SURESH
> wrote:
>
> > Dear all,
> >
> > My protein structure has 400 residues of which I want to calculate RMSD
> of
> > particular 2
It's 'r37-70 | r 120-167 | ...' so on and so forth.
On Mon, May 7, 2018 at 12:06 PM RAHUL SURESH
wrote:
> Dear all,
>
> My protein structure has 400 residues of which I want to calculate RMSD of
> particular 200 residues (approx) and they are not continuous. For example,
> from 34-70; 120-167;
Dear all,
My protein structure has 400 residues of which I want to calculate RMSD of
particular 200 residues (approx) and they are not continuous. For example,
from 34-70; 120-167; 180-210; For this how can I create an index file?
Thank you
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*B
On 1/5/17 3:40 AM, Aditya Padhi wrote:
Dear Gromacs users,
I am trying to evaluate entropic contributions for a protein-protein
complex using the gmx covar module and then gmx anaeig. When I directly run
the command "gmx covar -f prod.xtc -s prod.tpr -n index.ndx -o eigenval.xvg
-v eigenval.tr
Dear Gromacs users,
I am trying to evaluate entropic contributions for a protein-protein
complex using the gmx covar module and then gmx anaeig. When I directly run
the command "gmx covar -f prod.xtc -s prod.tpr -n index.ndx -o eigenval.xvg
-v eigenval.trr -av average.pdb -l covar.log", the progra
On 3/1/16 4:27 AM, Nikhil Maroli wrote:
Dear all,
i have generated cyclic peptide nanotube in Lipid bilayer system and input
files for GROMACS from charmm-gui . 50 ns MD is performed and i would
like to study non bonded interactions, when i invoke gmx energy- i got 50
options ,but none of th
Dear all,
i have generated cyclic peptide nanotube in Lipid bilayer system and input
files for GROMACS from charmm-gui . 50 ns MD is performed and i would
like to study non bonded interactions, when i invoke gmx energy- i got 50
options ,but none of them contain option such as
Protein-Membrane,m
On 5/26/15 2:32 PM, Giannis Gl wrote:
Dear all,
I am very amateur in GROMACS, so please forgive my silly question.
I want to group the following atoms
ATOM 2285b C1 LIG X 6 32.880 59.958 110.850 0.00
0.00
ATOM 2285c CL1 LIG X 6 31.972 61.400 110.520 0.00
0.00
ATOM 2285d
Dear all,
I am very amateur in GROMACS, so please forgive my silly question.
I want to group the following atoms
ATOM 2285b C1 LIG X 6 32.880 59.958 110.850 0.00
0.00
ATOM 2285c CL1 LIG X 6 31.972 61.400 110.520 0.00
0.00
ATOM 2285d N1 LIG X 6 32.318 58.744 110.53
Dear all,
I want to calculate the diffusion coefficient in the bulk based on Green-Kubo
relation. Now I want to use :
g_velacc -acflen 1001 -nonormalize -mol -n index.ndx -s topol.tpr -o vac.xvg
I have got different information about index.ndx file . should it contain
molecule numbers? Or
On 3/22/14, 7:41 PM, shivangi nangia wrote:
Hello All,
I have a question regarding case sensitivity for index file group names.
If I have a group named "l"ipid (i.e. lipid) in the index file but I have
it as "L"ipid (i.e. Lipid) in the .mdp file, does that matter?
I am not getting any errors
Hello All,
I have a question regarding case sensitivity for index file group names.
If I have a group named "l"ipid (i.e. lipid) in the index file but I have
it as "L"ipid (i.e. Lipid) in the .mdp file, does that matter?
I am not getting any errors while running any gmx command but I feel my
sys
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