I often use 4 fs with all-bonds and virtual sites, especially if lacking
sampling is a greater source of error than the kinetic energy being slightly
off.
Erik
On 15 Aug 2013, at 20:58, Michael Shirts wrote:
> I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic
> e
* Time
* Ac(hbond) with correction for the fact that a finite system is being
simulated.
* Ac(hbond) without correction
* Cross correlation between hbonds and contacts (see the papers by
Luzar&Chandler and van der Spoel that are mentioned in the stdout from g_hbond)
* Derivative of second column.
It's just the xvv file. g_wham uses the letter 'z' to denote the reaction
coordinate.
Erik
On 2 Jul 2013, at 11:32, battis...@libero.it wrote:
>
>
>
>
>
>
> Dear users and experts
>
> I'm doing an umbrella-samplig calculation to obtain the PMF when two
> structure (A and B) are at vario
…or the hydrogen-bond kinetics of your system may not fit the Luzar-Chandler
model for whatever reason.
Erik
On 17 Jun 2013, at 13:22, Erik Marklund wrote:
> Hi,
>
> Yes, the forward and backward rate constants are for hydrogen-bond breaking
> and reforming. You seem to h
Hi,
Yes, the forward and backward rate constants are for hydrogen-bond breaking and
reforming. You seem to have too poor statistics to draw conclusions about the
backward rate, however. You probably need to simulate longer.
Erik
On 15 Jun 2013, at 00:38, learnmd wrote:
> Hi,
>
> I have run
Hi,
No, I'm afraid not. pull-dim not only determines what components are to be
printed, it also determines in what dimensions the force is to be applied
during the simulation.
Erik
On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez
wrote:
> Dear Gromacs Users,
>
> I runned and Umbrella Sampli
has no -ver option.
> I also found out this link
>
> https://gerrit.gromacs.org/#/c/687/
>
> but dont know how to install/use it.
>
> Or maybe I can install DsspOld and see?
>
>
>
> On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund wrote:
>
>> Search a
Erik
On 12 Jun 2013, at 11:17, Nikunj Maheshwari wrote:
> Yes I did searched. But for most people, there were issues regarding the
> path or wrong DSSP.
> DSSP runs for me, but do_dssp does not.
>
>
> On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund wrote:
>
>> Hi,
Hi,
Search the mailing list. This problem and its solution has been repeatedly
discussed.
Erik
On 12 Jun 2013, at 10:31, Nikunj Maheshwari wrote:
> Dear all,
>
> I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> I am trying to use it for do_dssp command but get the foll
to install
old_dssp which is available through the dssp webpage.
Erik
On 7 Jun 2013, at 10:20, shika wrote:
> Hi Eric,
>
> I'm using gromacs 4.5.5.
> Is it the version is different for dssp?
>
> Thanks
>
> On Fri, Jun 7, 2013 at 3:41 AM, Erik Marklund [via GROMACS
HI,
What version of gromacs is this? DSSP changed its syntax a while back and we
had to adjust do_dssp accordingly. You may have a mismatch between gromacs and
dssp versions.
Erik
On 7 Jun 2013, at 08:42, Nur Syafiqah Abdul Ghani wrote:
> Hi All,
>
> I already done the MD production so I wa
Hi James,
Not related to the integration stability as such, but since the vsites affect
the hydrogens by definition perhaps g_hbond can reveal systematic differences
between simulations with and without vsites. I believe Feenstra et al did this
in the paper describing vsites in the first place.
How about running with -noappend?
On 1 Jun 2013, at 13:59, vidhya sankar wrote:
> Dear Justin Thank you for your previuos reply
> I am
> using gromacs 4.6 AMD 8 core processor
>
> When I run restart My run from the Checkpoi
"gcc" is probably still your old version. The new one would probably be called
"gcc-4.7" or similar.
Erik
On 30 May 2013, at 15:15, vidhya sankar wrote:
> Dear Justin and other gromacs users ,
> Thank you
> for your Previous
g hydrogen bonding energy, but I haven't see any "flag command"
> could give a output of "hydrogen bonding energy" file. Is it still under
> development?
>
>
> 2013/5/24 Erik Marklund
>
>> Hm. That is peculiar. The source code has the answer of course
rystal structure, which I
> should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512
> hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows
> that the summation of population is 200.
>
>
> 2013/5/24 Erik Marklund
>
>&g
Hi,
See below
On 24 May 2013, at 11:45, CHEN Pan wrote:
> Dear Gromacs users,
>
> I am confused about the g_hbond tools.
>
> 1) When I use "-dist" to get the distribution of hydrogen bonding distance,
> I found that the summation of the population is always 200 (the y-column
> below). I am no
Hi,
Just to clarify: The third column are the number of acceptor-donor pairs that
fulfil the distance criterion but not the angle criterion.
Erik
On 24 May 2013, at 09:06, CHEN Pan wrote:
> Hi Maggin,
> The middle column is the total number of hydrogen bonds in your system
> under the definit
Hi,
I have achieved good energy conservation in NVE simulations. This was single
proteins in the gas phase, using infinite cut-offs, constraints applied to
hydrogens, 0.5 fs or 1.0 fs time steps, double precision and virtual sites if
I'm not mistaken. We had problems with energy conservation fo
Hi,
For particles that diffuse more than half a box length between frames will
appear as if they haven't moved much, assuming you have periodic boundary
conditions.
Erik
On 22 May 2013, at 11:41, Anna Akinshina
wrote:
> Dear Gromacs Users,
>
> I have a question interpreting obtained msd da
g_hbond and g_hbond -contact
Erik
On 22 May 2013, at 05:37, Vishal Kumar Jaiswal wrote:
> Hello gromacs users
>
> I performed a 1 ns simulation of N-isopropylamide in water. Now i wish to
> calculate the average no of water molecules(averaged over entire
> trajectory) within a certain distance
Hi,
To get useful help with this issue you need to provide a more informative
description of what when wrong, i.e. what gromacs tool was invoked and what
input was used.
Erik
On 20 May 2013, at 10:59, Pruthvi Bejugam wrote:
> Hi all,
>
>I want to perform a RNA (Just RNA no p
HI,
s0, s1,… is (xm)grace codes that refer to the different datasets in the file.
Gromacs prints the datasets as different columns. I suggest opening the file
with xmgrace -nxy yourxvgfile.xvg. As for the -life option, the results are
based on a too wimple kinetic model for most applications.
Hi,
Have a look at the following article. It describes a non-standard box type that
seems ideal for your application. I don't know what is the latest gromacs
version where it is implemented, however.
Author = {Wassenaar, TA and Mark, AE},
Title = {{The effect of box shape on the dynamic propert
/home/dssp seems like a strange path. Are you sure you set DSSP correctly?
Erik
On 8 May 2013, at 15:19, Sainitin Donakonda wrote:
> Hello,
>
> I am trying to secondary structure analysis using DSSP in gromacs so i
> followed this procedure
>
> First I downloaded dssp
>
> wget ftp://ftp.cmb
I really don't think thats possible at the moment. All interactions in Reax, if
I recall correctly, are dependent on bond order, which is not an implemented
concept in gromacs.
Erik
On 6 May 2013, at 12:51, Sathish Kumar wrote:
> hai
> i would like to use Reax force field,can we use r
protonation/deprotonation equilibria is accounted for while my question
> relates to the typical constant protonation MD where each titratable group
> remains in one protonation state throughout the simulation. Please educate
> me
> Shahid
>
>
> On Fri, May 3, 2013 at 6:22 P
resting take on sampling multiple protonation states.
Best,
Erik
On 3 May 2013, at 14:05, shahid nayeem wrote:
> Thanks a lot Erik. Could I get some reference based on which you say that
> much of the structural biology will be largely unaffected.
>
> Shahid
>
>
> On Fri, M
If I recall correctly it uses the seed provided in the mdp file. If no seed is
provided it uses the process id for seeding. The manual explains the details.
Erik
On 3 May 2013, at 08:00, Preeti Choudhary
wrote:
> hey this is regarding random seed used in md.this is when it selects the
> intia
There's no general answer to that. Proton conductivity measurements, for
instance, will be horribly wrong without dynamic protonation. Much (but not
all) structural biology, however, will be largely unaffected.
Erik
On 3 May 2013, at 04:30, shahid nayeem wrote:
> Dear all
>
> Can someone enl
You seem to be using a 2 fs time step. It's difficult to achieve stable
integration using 2 fs time steps in vacuum. Please provide more information
about your simulation parameters.
Erik
On 2 May 2013, at 14:40, Souilem Safa wrote:
> Dear Gromacs users ,
> I did the simulation of a single mo
Average coordinates are problematic and not generally representative. Consider
for instance the average coordinates of a methyl group connected to X. The
rotation around the C-X bond causes the average positions of the hydrogens to
line up. Consider using g_cluster to find representative structu
Hi,
Could you please clarify if the hbond existed in frames for which g_sdangle
reported a ADH-angle above 30 deg?
Also, bear in mind that the -merge flag is on by default, so another hydrogen
may bridge the donor-acceptor gap.
Erik
On 24 Apr 2013, at 21:09, kim2811 wrote:
> Hi, is there an
There's a known oscillation in the ACF that occurs at ~100 fs or so. Is that
what you see?
Erik
On 9 Apr 2013, at 18:02, Nilesh Dhumal wrote:
>
>
>> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
>> wrote:
>>
>>> Hello,
>>>
>>> I am calculating the hydrogen bond autocorrelation function us
nal temperature spacing for the run? Did you get the
> fitted values using polynomial fit?
> Was the run completed?
>
> On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund wrote:
>
>> I've tried one with 666 aa, but with no publishable results.
>>
>> On 9 Apr 20
I've tried one with 666 aa, but with no publishable results.
On 9 Apr 2013, at 09:47, Nikunj Maheshwari wrote:
> Dear all...
>
> Does anyone has any idea what is the maximum protein size for which a
> successful REMD run has taken place?
> We have went through lots of research papers, but could
The gromacs web page links to this server for REMD temperature generation:
http://folding.bmc.uu.se/remd/
On 9 Apr 2013, at 08:34, Nikunj Maheshwari wrote:
> Hi. Glad to know that your REMD was successful. We are trying to do the
> same, but are stuck in between.
> Can you tell us, how did you
I always do. There's nothing particular about umbrella sampling in this respect.
On 4 Apr 2013, at 17:33, raghav singh wrote:
> Hello Fellow Users,
>
> I have a question regarding US simulation.
> I am interested to know that can I treat hydrogens as virtual sites in US
> simulations??
> I have
It is, and I think there was in fact some experimental/private branch that
dabbled with this. It hasn't gone into the official releases yet and there is
no guarantee that it will.
Erik
On 4 Apr 2013, at 14:10, nahren manuel wrote:
> Sorry to bother you all once again. As there were no replies
Yes.
On 3 Apr 2013, at 04:07, Nilesh Dhumal wrote:
> Hello,
>
> I am calculating the hydrogen bond life time for my system.
>
> Do program consider the hydrogen bond criteria for calculation of
> autocorrelation function?
>
> Nilesh
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs
On 2 Apr 2013, at 13:30, Justin Lemkul wrote:
>
>
> On 4/2/13 7:13 AM, rama david wrote:
>> Dear friends,
>> I am naive to the Replica exchange Molecular dynamics ( REMD).
>> I have plan to use REMD for temp. 310-320 K to my system.
>> I thoroughly search the Mailing-list Archive fo
Hi,
I suggest contacting people in Johan Åqvist's lab. I'm sure they know exactly
what pitfalls there may be with regards to the choice of LIE parameters and
what has been done for different types of molecules.
Erik
On 26 Mar 2013, at 02:42, Vishwambhar Bhandare wrote:
> dear gromacs users,
13 at 9:28 PM, Erik Marklund
wrote:
I could see how -merge (on by default) could lead to this. Have you
tried
-nomerge?
Erik
On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote:
Dear Users,
As suggested earlier by Erik I used 4.6 to calculate the hydrogen
bonds.
Still the
Total intra-pro
+MS +SS)
hydrogen bond.
Is there any other solution?
Thank you
Kavya
On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M
wrote:
Dear Sir,
Sure I will try with 4.6. presently I am not able to download it.
Thank you
kavya
On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund
wrote:
There were a
On Mar 19, 2013, at 11:45 AM, Justin Lemkul wrote:
On 3/19/13 5:44 AM, 라지브간디 wrote:
Anyone tell me how do I freeze the particular residues in NPT-NVT
equillibrium steps ? I want them in same conformation as pdb for
further production run ? Thanks in advance
Use freezegrps or strong posi
Hi,
I believe there is no force output for constraint pulling. Try umbrella.
Erik
On Mar 18, 2013, at 3:28 PM, raghav singh wrote:
Hello Fellow Users,
I am trying to pull a DNA molecule. I have fixed one end and trying
to pull
the other one using this .mdp file.. force output is all zeros
Gromacs currently use OpenMP and/or MPI with it's own wrappers for
parallel computation. There is a general framework being developed for
parallelizing analysis tools, but I don't know the specifics and I
beleive it's not ready for use yet.
Is that helping you?
Erik
On Mar 14, 2013, at 3:
Do you really mean compile time? If so, issue make -j X (where x is
the number of jobs used for building).
If you mean runtime then the easiest thing is to split your trajectory
in parts and run the processes in parallel, then patch the results
together. That's if the calculations can be do
Restraints allow, by definition, for slight deviations.
Erik
On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote:
Dear gmx users,
I want to use restraints on backbone of my protein to keep its
secondary structure during minimization and equilibration steps. To
do so, I generated backbone-re
Hi,
You also need to consider the ensemble you want to investigate. If you
simulate under constant energy you need a shorter timestep than you
would have in solution and probably double precision. In the articles
I list below we used a timestep of 0.5 fs and 1 fs, respectively, and
double
On Mar 7, 2013, at 2:59 AM, Justin Lemkul wrote:
On 3/6/13 8:57 PM, Vishwambhar Bhandare wrote:
dear gromacs user,
how i can do binding free energy calculation for RNA duplex in
gromacs?
any tutorial for the same??
Free energy calculations involving interactions between
macromolecules
bit confusing though!
Thank you
kavya
On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund
wrote:
To clarify: the -hbn output is not very indicative of how many
contacts
there were since some of them could be present in one frame but
absent in
99. The -num option, however, provides the numbe
To clarify: the -hbn output is not very indicative of how many
contacts there were since some of them could be present in one frame
but absent in 99. The -num option, however, provides the number of
contacts over time, and its time average probably tells you much more
in this case.
Wh
From the manual it seems that oscillating electric fields are not yet
implemented, which surprised me. I've seen colleagues use such in
gromacs, but that may have been in-house modifications. Should be
fairly simple to implement though.
Erik
On Mar 4, 2013, at 11:30 PM, raquick wrote:
Gr
As Justin implied, -merge could potentially make a factor of 2. Try
g_hbond -nomerge.
Erik
On Mar 4, 2013, at 4:02 PM, bipin singh wrote:
Thanks for the reply.
The difference is almost double, through g_hbond the average number of
contacts are 1821 and through g_mindist it is 3643. The calcu
xtra space / 35SOL/d (instead of /
35SOL/d)
by this sed will remove 35SOL not 135SOL.
regards,
On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund
wrote:
Hi,
Then the problem lies in automating what molecules are to be removed,
right? Try g_select or look into trjorder.
Erik
On Mar 1,
.0,
just
decided to try an older version before going into the trouble
itself...
Kind of coward, I know, but the troubles with that version are already
reported so that I thought things would be easier :)
Thank-you a lot for your comments
2013/3/1 Erik Marklund
Interesting. Perhaps the
I get I plot very small,
where one barely can see the colour code and the legend is sooo big.
Does
anyone know how to change that?
2013/3/1 Erik Marklund
What happens if you execute the command (/usr/local/bin/dssp/ -i
ddQ3PqtX
-o ddR1HavD) in your terminal?
Erik
On Mar 1, 2013, at 1
, 2013 at 3:09 PM, Erik Marklund
wrote:
On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
Dear Erik,
so you can filter out the unwanted residues there instead of
using an
index file.
There are thousands of water to be removed so simple
On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
Dear Erik,
so you can filter out the unwanted residues there instead of
using an
index file.
There are thousands of water to be removed so simple commands like
sed
exhausts when I run
a new gro
without the residues mentioned in index file?. I used this editconf -f
my.gro -n index.ndx -o del.gro .
thanks,
This gave me del.gro having residues mentioned in index file. But I
want
del.gro file without the residues mentioned in index file.
On Fri, Mar 1, 2013 at 2:48 PM, Erik Mar
What happens if you execute the command (/usr/local/bin/dssp/ -i
ddQ3PqtX -o ddR1HavD) in your terminal?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3Pqt
The ndx format is really simple. You can easily script your way to a
new index group as long as the selection of atoms can be automated.
Furthermore, the gro format is also simple, so you can filter out the
unwanted residues there instead of using an index file.
Erik
On Mar 1, 2013, at 1:4
With -ver, just like it says. do_dssp -h explains how. What dssp
version do you have?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /de
Hi,
Search the mailing list archives. This is admittedly confusing and has
been discussed several times.
Best,
Erik
On Feb 22, 2013, at 7:30 AM, Kavyashree M wrote:
Dear users,
I just wanted a small clarification whether the order of elements in
matrix
(-hbm) corresponds to reverse orde
On Feb 22, 2013, at 1:13 AM, Justin Lemkul wrote:
On 2/21/13 6:24 PM, Yun Shi wrote:
So in umbrella sampling, does it really matter if the vector
connecting the COMs of protein and ligand is NOT parallel with the
vector of the pulling force (although the pull rate is 0)?
I guess as long as t
Hi,
For an analysis tool you would use the functions in tpxio.h for
reading tpr files. Then you don't need to bother about filling out the
inputrec yourself.
Erik
On Feb 21, 2013, at 7:48 PM, shavit wrote:
I think your'e right. I'm currently trying to make it work, but am
not
really s
Hi,
What difference does it make? All coordinates are translated by a
fixed vector. There is no need for a reference point.
Best,
Erik
On Feb 21, 2013, at 3:31 PM, Kieu Thu Nguyen wrote:
Dear all,
I am not clear about the option -translate following editconf tool.
Whether the coordinates
On Feb 20, 2013, at 9:58 PM, Erik Marklund wrote:
Hi,
pdb2gmx generate the connectivity from the residue and atom
sequences (the file format specs state the order in which they
appear) and the distances between atoms. This is fairly robust as
long as the coordinates aren't unusuall
Hi,
pdb2gmx generate the connectivity from the residue and atom sequences
(the file format specs state the order in which they appear) and the
distances between atoms. This is fairly robust as long as the
coordinates aren't unusually bad. For instance, if two carbons are
located at ~1 C-C
Ponder this: What is the pressure of vacuum?
On Feb 19, 2013, at 12:32 PM, raji wrote:
for vacuum simulation , no need to specify cut-offs right. am using
8x8x8 box
and if we don't specify barostat it will again be a NVT simulations
right.
vacuum simulations can be done only in NVT ??
sorry
Using a barostat for vaccum simulations is very peculiar.
Erik
On Feb 19, 2013, at 10:55 AM, Rajalakshmi.C wrote:
hi all,
i am trying to simulate polymer chains in solvent and vacuum media
using 45a3
forcefield. for vacuum simulation i used different md parameters
than that of
solvent med
wrote:
Hello Sir,
I used C-alpha atoms.
Kavya
On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund >wrote:
Hi,
With -r2 one can provide a second, larger, cutoff so that contact
kinetics can be analyzed within the Luzar-Chandler framework that
were
designed for hbonds.
What index gr
vyashree M
wrote:
Hello Sir,
I used C-alpha atoms.
Kavya
On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund >wrote:
Hi,
With -r2 one can provide a second, larger, cutoff so that contact
kinetics can be analyzed within the Luzar-Chandler framework that
were
designed for hbonds.
What
). With a distance cut off of 0.5nm there should have been
more
number
of contacts. And what is the difference in using -r only or -r2 only
and
combining -r
and -r2?
Thank you
Kavya
On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M
wrote:
Thank you!
On Thu, Feb 14, 2013 at 3:38 PM, Erik
On Feb 14, 2013, at 2:01 PM, Justin Lemkul wrote:
On 2/13/13 5:23 PM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul
wrote:
On 2/12/13 9:57 AM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul
wrote:
On 2/12/13 9:40 AM, Steven Neumann w
Perhaps g_hbond -contact will do what you want.
Erik
On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:
Dear users,
How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr writes
with the option -sep.
I tried using g_mdmat but it give
It shouldn't generate output. It will make your system find your
gromacs installation, however. Try e.g. "which mdrun".
Erik
On Feb 13, 2013, at 5:06 AM, David Sáez wrote:
Thanks for your answer Justin. I followed your advice:
When I type
*$ source /usr/local/gromacs/bin/GMXRC*
*$*
Nothing
Hi,
I have used MacroMolecule Builder for similar things.
Erik
On Feb 13, 2013, at 4:41 AM, zugunder wrote:
Hi,
I am sorry if this topic is not relevant for GROMACS forum, but I hope
someone has faced the same problem before and could give me some
advice...
I need to simulate a relativel
Try virtual sites constructions.
On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote:
Dear All,
I need to define interaction sites on the center of C-H bonds instead
of nuclei of each atom. The main reason was that non-bonding
parameters (sigma and epsilon) have been parametrized in these centers
I've never seen good parameters for nucleic acids. There might be
such, but none that ship with gromacs as far as I know.
Erik
On Feb 7, 2013, at 4:25 AM, 김현식 wrote:
Dear experts,
Hello!
Is it possible to run RNA md with GBSA?
Thank you.
bestKim. --
Hi,
Perhaps a side point: Temperature and pressure can not be seen as
constraints to the system at any given instant in the sense that e.g.
the instantaneous kinetic energy perfectly match the temperature at
every time step just because you have a thermostat. Time and ensemble
averages wi
On Feb 5, 2013, at 8:22 AM, bipin singh wrote:
Hello All,
Please let me know whether is it possible to manually assign the
velocity
for each atom in the simulation instead of generating through gen_vel
option.
If the preceision of a gro-file is sufficient you can use such for
manually s
HI,
It should read "trjconv". And all analysis tools have the -b and -e
flags for excluding the start or the end of a trajectory.
Erik
On Feb 4, 2013, at 7:00 AM, Emanuel Birru wrote:
Use trajconv
http://manual.gromacs.org/online/trjconv.html
-Original Message-
From: gmx-users-bo
Hi,
If you don't care about the exact distances, but rather the time the
groups spend within a certain distance, g_hbond -contact can be useful.
Best,
Erik
On Feb 3, 2013, at 6:36 PM, James Starlight wrote:
Justin,
1 )for example I want to select in index file only all asp, glu and
his re
Short answer is to inspect your complex with VMD or Pymol (or some
other viewer). Pymol takes pdb input, so unless your structure is
contained in a pdb file you must convert it with e.g. trjconv first.
If you want a single frame you need to extract one form your
trajectory, or, if the final
, Erik Marklund
wrote:
Hi. What version was this? Have you tried with -nomerge?
Erik
On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:
Dear users,
While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS
On Jan 25, 2013, at 5:53 AM, Shima Arasteh wrote:
Thanks for your reply.
I want to chose one of the 5 conformers from a NMR PDB. As I studied
in literature, the average structure could be selected regarding
RMSD values and the go on with selected one to simulate in in water,
lipid bilay
g_traj -nox -noy if I recall correctly.
On Jan 21, 2013, at 4:10 PM, Albert wrote:
hello:
I would like to make statics for an atom along Z-axis. I am just
wondering how can I to do this in Gromacs?
thank you very much
best
Albert
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Hi. What version was this? Have you tried with -nomerge?
Erik
On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:
Dear users,
While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM
Hi,
If you're simulating in the gas-phase, how come you want implicit
solvent?
Erik
On Jan 11, 2013, at 5:07 AM, Sanku M wrote:
Hi,
I am trying to do implicit solvent simulation for a protein in gas-
phase. I have a few questions :
1) should I use sd integrator?
2) should I also use n
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> Felipe
>
> On 11/22/2012 11:12 AM, Erik Marklund wrote:
>> It will depend on the integration algorithms, parallelization, etc. The
>> equations are deterministic, but numerical differences may arise e.g. from
>> different ordering of floating point numbe
Felipe
>
> On 11/22/2012 10:04 AM, Erik Marklund wrote:
>> Stochastic and chaotic are not identical. Chaotic means that differences in
>> the initial state will grow exponentially over time.
>>
>> Erik
>>
>> 22 nov 2012 kl. 09.52 skrev Felipe Pineda
et two results with large differences.
>>>>>
>>>>>So I am just wondering how to perform repeated MD in Gromacs in a
>>>>> correct way so that our results can be acceptably repeated?
>>>>>
>>>>> thank you very much.
>>
macs.org.
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46
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