coupling
tc_grps = system
tcoupl = no ;nose-hoover
tau_t= 0.1
ref_t= 300
;Pressure coupling
pcoupl = no
optimize_fft = yes
Any suggesions are really welcome.
Thank you.
Regards,
Andrea
Thank you for your hints. I'll give it a try right now.
Regards,
Andrea
2010/3/1 Berk Hess
> Hi,
>
> Shake is not relevant for water and also a time step of 2 fs should be
> fine.
> The cut-off's are the problem. You have a buffer size of 0.1 nm,
> which is alre
I don't think the atom number is the problem. I also have systems with more
than 9 atoms, and in the gro file the atom number after 9 is reset
to 0, but that was never a problem for the simulations. I would check the
parameters again, but I don't have a more exact answer to your problem.
2
Hi there,
for european users you may think to apply to hpc-europa
(http://www.hpc-europa.eu/) and http://www.deisa.eu/
Regards
andrea
---
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c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132
le inside of the Cu2+ cluster in a second study.
Any suggestion, comments and anything else are very welcome.
Thanks in advance
Regards
andrea
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
Hi Tsjerk,
thanks for the usual useful suggestions! Probably I will go for that, add an
harmonic bonds between
Cu2+ and N-HIS and I will think how to hand the charges too.
Probably this is the less worst solution for now.
Thank a lot,
Regards
andrea
Tsjerk Wassenaar wrote:
> Hi And
Hi Pablo,
I would write .rtp entries and so on for each monomer.
You copy the modified files into your working directory.
Have a great day,
Andrea
2009/10/6 Englebienne, P.
> Hi all,
>
>
>
> I’m looking to perform simulations on a series of synthetic co-polymers
> conta
hat I could fill before running the analysis?
3)Should I use another type of box? Trasform the trajectory with some
pbc keywords (I've also tried -ur compact without luck)...
Thanks in advance and sorry for the long message
Andrea
___
gmx-users ma
have no mismatch of ionsname in different files. I hope this helps.
Regards
Andrea
2009/11/17 Arden Perkins
> I am an undergraduate student and I am still learning to use GROMACS. When
> I add my ions to the solution (using genion) by the procedure described in
> the funnel web spider tut
if I have misunderstood the use of periodic_molecules: does the
molecule need to be periodic in the 3 X- Y- Z- directions or it can be periodic
just along one directions, as in the case of CNT?
Any help is more appreciated.
Andrea--
gmx-users mailing listgmx-users@gromacs.org
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`./src/kernel//.deps/restraint_waterbridge.Po': No such
file or directory
touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file or
directory
touch: cannot touch `./src/k
r:
hi (-1000.00) <= lo (0.00)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Could you please help me?
Thanks
Andrea
--
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Andrea Carotti
Dipartimento di Chimica e Tecnologia del
--
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Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele
Centro di Genomica Traslazione e Bioinformatica
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
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20132 Milano
Italy
Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site
have a full set of matching .cpt
files, but not with consistent names. Use gmxcheck to see the times.
Mark
On Fri, Apr 19, 2013 at 3:24 PM, andrea spitaleri
wrote:
Hi there,
I am performing a remd (8 replica) using gromacs-4.5.3
Unfortunately, the job crashed for a problem with our cluster
Hi,
have look to:
http://www.plumed-code.org/
and
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
Basilica San Raffaele, 3P 34R
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
www.biomolnmr.org
Tel: 0039
r any help
and
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Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Italy
Tel: 0039-0226434348
Fax: 0039-02264
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Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
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Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site
etc) hydration layers around a protein. I am curious to
know if there is any way to obtain/guess the thickness of this layer.
How does one defines the thickness ?
Thanks,
Bala
--
C. Balasubramanian
--
***
Andrea Coletta
contains force field
parameters for Mn 2+ .
Thanks
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Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
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Italy
Tel: 0039
Many thanks in advance and best regards
Anna
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Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele
Centro di Genomica Traslazione e Bioinformatica
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olg
Hi,
I suggest you to visit the plumed webpage and ask to the mailing list.
http://www.plumed-code.org/
best
and
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
Basilica San Raffaele, 3P 34R
Via Olgettina 58
20132 Milano (Italy)
http
missing
in the .top file is defined in the .rtp. So I have really no clue what is
wrong. I runned pdb2gmx also in debug mode, but the log file seem ok to me.
Please give me a good idea :o)
Thanks in advance.
Andrea
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proper dihedrals, the impropers are OK).
Thanks for your help.
Andrea
RTP.pdf
Description: Adobe PDF document
TrimerTOP.pdf
Description: Adobe PDF document
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1920 1gd_1
25181924 1gd_1
18192021 1
18192423 1
Cheers,
Andrea
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Please search the
Strange enough, those dihedrals are there, but the dihedral between
atoms 2 9 10 and 17 is missing (in the main chain), altough defined in
the PS residue (as -CH CH2 CH +CH2). I am still clueless...
Greetings,
Andrea
2008/10/27 Justin A. Lemkul <[EMAIL PROTECTED]>:
> Well, there&
2 91011 1
9101116 1gd_1
9101718 1gd_17
10171825 1gd_17
17181924 1gd_1
Best regards,
Andrea
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residues?
And are the 2 definitions (with +CH2 and CB at the end) equivalent,
taking in acount that we define also an improper of type gi_2 around
the CH atom?
Cheers,
Andrea
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and
angles) already when I run pdb2gmx?
Thank you in advance for any contribution.
Best regards,
Andrea
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Dear users,
I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and
the following parameters (only a few are given):
; RUN CONTROL PARAMETERS
integrator = md
tinit= 0
dt = 0.002
nsteps = 125000
comm-mode
I thought so. Thank you very much!
Cheers
Andrea
2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED]>:
>
>
> Andrea Muntean wrote:
>>
>> Hello there,
>>
>> I have a practical question regarding the mdp file, regardless the
>> system to simulate. Before I
want to run another simulation, with the same input, only with
small changes in the mdp file (like number of steps or so), do I have
to each time modify the input .mdp and run grompp, or is it enough if
I modify mdout.mdp?
Best regards,
Andrea
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!
Andrea
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Thank you. I will do so.
kind regards,
Andrea
2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED]>:
>
>
> Andrea Muntean wrote:
>>
>> I am simulating one chain of PS. The box is produced by pdb2gmx. If I
>> run simulations with timestep 0.1 fs up to 0.4 fs every
Hi gmx-users,
We are using the version 3.3.3. Is there also a posibility to have pbc
only in xy direction (as I saw it is possible in Gromacs 4.0)? The
manual says nothing about that.
Thank you in advance.
Best regards,
Andrea
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Hi Berk,
that is a good idea. Thank you for your answer.
Cheers,
Andrea
2008/12/11 Berk Hess <[EMAIL PROTECTED]>:
> Hi,
>
> This is not possible in 3.3.
>
> But in practice you almost never need this,
> since it is far more efficient to use pbc=xyz and have a slab of
not listed here)
I hope that will help.
Andrea
2009/2/5 varsha gautham :
> Hello justin,
>
> Am sorry to say that its not useful.But what i mean is that the rtp
> constructed manually is building up the polymer and generating topology
> files and gro files.
> But when i look into
Hi Andrew,
I would do it with editconf with the same options.
Regards
Andrea
2009/3/11 Andrew Voronkov :
> Dear GROMACS users,
> is there a possibility to convert .gro files directly to PDB? Or I can do it
> only with .tpr?
> I've tried gro2pdb -f conf.gro -o conf.pdb
>
Hi all,
perhaps a silly question but i didn't find the correct way to calculate
the variance explained by each eigenvec in ED analysis.
Could someone point me out to a correct tool/option to use.
I'm using gmx v3.3.
Many thanks
Andrea
--
¯¯¯¯¯¯¯¯
Andrea Carotti
Dipar
Dear Dr. Wassenaar,
many thanks for your kind reply.
Andrea
--
Andrea Carotti
Dipartimento di Chimica e Tecnologia del Farmaco
Università di Perugia
Via del Liceo, 1
06123 Perugia, Italy
phone: +39 075 585 5169
fax: +39 075 585 5161
www http://rpg.unipg.it
personal www
i have a problem with gromp
someone can elp me? thanks..
error_grompp
Description: Binary data
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generating
the new tpr on my cluster. I did it and it runs, however I was wondering about
the physical and
chemical reliability.
thanks in advance
Regards
andrea
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR
also not very clear to me.
thanks in advance
Regards
andrea
Berk Hess wrote:
> Hi,
>
> As mdrun will tell you in stderr and md.log when you try continuing,
> you will have exact continuation, but not binary identical (which you would
> not have anyhow if you use dynamic load
-fontsize = 16
y-font = Times-Roman
y-tickfontsize = 10
y-tickfont = Helvetica
Any help_??
thanks in advance
andrea
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-------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStati
CNT as well as in the dynamic in
vacuo.
hope in some answers. Thanks
Andrea
--
Dr. Andrea Minoia
Chemistry of Novel Materials
Uneversity of Mons, UMONS
Parc Initialis, Avenue Copernic 1
B-7000 Mons, Belgium
Mail: mino...@averell.umh.ac.be
Tel: +32 65 373859 Fax: +32 65 373861
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you tell me what else you need?
Again, thanks.
cheers,
Andrea
In the absence of information about your ensemble (from your .mdp file or a
> description, hint hint) I'd guess it's because you've excluded all the
> non-bonded interactions for which you had non-zero paramet
xcl =
---
> energygrp_excl = CNT CNT
2) create the index file for the subsystem
3) rerun grompp to create the new tpr for all the system, without
energygrp_excl
4) use the new tpr with tpbconv to create the simulation file for the
subsystem
5) adjust the trajectory
6) run mdrun -rerun
ocess?
Thank you in advance
N.V.
--
-----
Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Italy
Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
http://ww
ch Schloar,
Prin. K. M. Kundnani College of Pharmacy,
Colaba, Mumbai-05.
Cont. No. +91 9769051866
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Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
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I
Copenhagen
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-----
Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Italy
Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
http://www.linke
Dear Nisha,
have look to the plumed plugin in gromacs:
http://merlino.mi.infn.it/~plumed/PLUMED/Home.html
you can perform US and Metadynamics calculations.
Hope it helps
and
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of
range since I am not neither using time nor ensemble averages nor
multiple dist restraints.
thansk in advance for any help
and
----
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
.2643.4461 – www.sanraffaele.org--- Begin Message ---
Hi there,
thanks for that. It makes clear.
Regards
and
--------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
c/o DIBIT Scientific Institute
Biomolecula
ERSION 4.0.7
Source code file: qmmm.c, line: 191
Fatal error:
Ab-initio calculation only supported with Gamess or Gaussian.
---
***
What can be the solution?!
Thank you
Andrea Coletta
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; coordinates every 5ps to xtc
xtc-precision = 2500 ;
xtc-grps= complex;
Since the error is happening only for the continuing run, I am just wondering
if there is any reason for this.
thanks for any help
and
Andrea
>From the log file I do not see any errors. Everything seems fine. I have free
>room space in the hd too :)
I am just wondering whether the problem is in the xtc options (precision and
writing step)
thanks a lot
and
----
Andr
error,
but now it sounds a bit strange. I will ask for a long simulation 50ns without extending steps.
thanks in advance
regards
and
On 11/22/2010 05:44 AM, Roland Schulz wrote:
On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea
mailto:spitaleri.and...@hsr.it>> wrote:
Hi,
ye
,
Regards
andrea
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---
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Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
)
is there a way to do it with gromacs? I looked carefully in the manual and in
the mailing list too, but I couldn't find an option to do this
Thanks in advance,
Andrea
--
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Postdoctoral Associate
Dept. of Structural and Chemical Biology
Mount Sinai School of Medicine
Hi,
have look to this:
http://stein.bioch.dundee.ac.uk/~charlie/software/pdb-mode/pdb-mode.html
I found it very useful
regards
andrea
Wei, Xiupeng wrote:
> Dear GMX users,
> I have a basic question. I want to put two same box in x direction.
> So I need increase the number
ng lists.
Any clue about what's going on?
Thanks,
Andrea
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Please don't
Thanks Berk,
yes, it was an older version. And I did have separate pme nodes when
posre was working. So now I'm trying out the new CVS version.
Andrea
On Jul 21, 2008, at 1:53 PM, Berk Hess wrote:
Hi,
There was a bug with PME and position restraints in the CVS version,
but that has
-dd 4 4 4 option).
I hope this help in gmx debugging
Regards,
andrea
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
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Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
Tel: 0039
Hi again,
in addition to the previous post, 4.0_beta1 crashes using 27 cpus and option -dd 3 3 3, whereas it
goes fine using 24 cpus and not -dd option.
any clue?
Regards,
andrea
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Dulbecco Telethon Institute
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Hello everyone,
Does anyone have a script to do T-WHAM analysis of replica exchange
trajectories?
Any help would be great!
Thanks,
Andrea
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Hello,
we are trying to generate a polystyrene box. We have a homemade pdb file,
but the residues are not recognised. Have somebody a good pdb file or can
tell me what are the standard residues in Gromax?
Any other good hints are welcome.
Thanks a lot,
Andrea
I want to install fftw and gromax in my directory. Everything went ok, fftw
was installed without errors. When I configure gromacs I have the error:
cannot find fftw3f library.
I did use the CPPFLAGS and LDFLAGS.
Can somebody help me?
Thank you kindly in advance!
Andrea
rtp file for
Polystyrene? Which force filed would be more apropriate (united atoms)?
Thank you.
Andrea
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Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
Tel: 0039-0226434348/5622/3497/4922
correct
parameters in the *.itp file(s). But it is still not clear to me how to
define the conectivity between the monomers.
Can somebody help me? I saw there are some people simulating polymers with
gromacs. Please help!
Thank you for any help,
Andrea
y to do
so?
Regards,
Andrea
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hanks again for your help.
Best regards,
Andrea
2008/10/22 Mark Abraham <[EMAIL PROTECTED]>
> Andrea Muntean wrote:
>
>> I have a *pdb file for a polymer box which I want to use. I defined the
>> residues (the first, the last and the inner monomers).
>> Pdb2gmx runs
Thank you. I hope this helps me further.
My system is 32 polystyrene chains of 80 monomers.
Andrea
2008/10/23 Mark Abraham <[EMAIL PROTECTED]>
> Andrea Muntean wrote:
>
>> Thank you for your answer.
>> If I am looking at the PDB standard format and my file, I observe
It did work. Thank you!
Cheers,
Andrea
2008/10/23 Mark Abraham <[EMAIL PROTECTED]>
> Andrea Muntean wrote:
>
>> Thank you for your answer.
>> If I am looking at the PDB standard format and my file, I observe that I
>> have only one number between the type of
then i use trjconv to dump a configuration file at 70 ps it says:
WARNING no output, trajectory ended at 69
Is it normal? I don't mind to extract a configuration file at 69 ps, however i
was wondering if this
behaviour is normal or whether it is bug.
thanks in advance
Regards
a
...
gmx version 3.3.1
Regards
andrea
David van der Spoel wrote:
> andrea spitaleri wrote:
>> Hi all,
>> silly question. I have checked a trr with gmxcheck and I get this
>> output below:
>> Item#frames Timestep (ps)
>> Step701
>> Time
Hi,
however in md0.log the right time is reported (69 and not 70)
and
David van der Spoel wrote:
> andrea spitaleri wrote:
>> Hi all,
>> silly question. I have checked a trr with gmxcheck and I get this
>> output below:
>> Item#frames Timestep (ps)
>>
efficient volume should be 10x10x10? I cannot figure out how did you
retrieve this conclusion.
Thanks for your help anyway,
Regards
Andrea
--
-------
Andrea Spitaleri PhD
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Biomolecular NMR, 1B4
Via Olgettina
Hi,
why do not think about a beginners mailing list or gromacs for dummies?
of course this is my humble opinion to you guys
and of course I agree with you in searching **always before** in the list
archive ..
This is just a suggestion ...
Regards,
andrea
Berk Hess wrote:
> Maybe
advance
Regards,
andrea
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Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom
Hi sorry for the poor information.
I have used PME with rlist = rcoulomb = rvdw = 0.9 (as I said) and the
g_mindist is between the
protein-protein system
thanks
Regards,
andrea
David van der Spoel wrote:
> [EMAIL PROTECTED] wrote:
>> Hi all,
>> my rlist = rcoulomb = rvdw = 0.
115 (prerelease) (SUSE Linux)
Suse 10.2 2.6.18.2-34-default
I did not find any entry in the bugzilla.
Thanks
Regards,
Andrea
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
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Biomolecular NMR, 1B4
Via Olgettina
Hi,
okay I will submit the bugzilla.
Thanks
Regards,
andrea
David van der Spoel wrote:
> andrea spitaleri wrote:
>> Hi all,
>> I have suspicious that g_rdf is bugged or at least it has a problem
>> depending on the machine type.
>> In one pc works and in another it han
-homogeneous
situation?. In few words, after few nm there are not oxygen atoms interacting
with the ion.
Thanks
Regards
andrea
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
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Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano
Hi
which gcc have you used for compiling gromacs? I have the same problem in one
pc in which I have
build gromacs using gcc-4.1
Regards
andrea
Sampo Karkola wrote:
> Dear list,
>
> the genion program gets halted when I'm trying to replace the solvent
> molecules with
gcc-4.0.2 seems ok for gmx-3.3.1
I have also submitted in bugzilla a similar problem with g_rdf
Regards
andrea
Sampo Karkola wrote:
> Hi,
>
> the same one, gcc-4.1. Have you tried with other versions?
>
> Sampo
>
> andrea spitaleri wrote:
>> Hi
>> whic
Hi
yes I do use genion and g_rdf properly with 4.0.2
Regards
and
Sampo Karkola wrote:
> Hi,
>
> so you got genion working with 4.0.2?
>
> Sampo
>
> andrea spitaleri wrote:
>> gcc-4.0.2 seems ok for gmx-3.3.1
>> I have also submitted in bugzilla a similar pr
simulation
is to check whether the SS bond is present in your topology in order to be used
as it is during the
gromacs simulation. Check for the specbond.dat file
I hope that it helps
Regards
andrea
özge kül wrote:
> After making Md simulation and getting the rmsd,gyration.. analyzing
> grap
trr in order to analyze for
instance the violated NOE.
Skip last question, sorry :)
Regards
andrea
pkmukher wrote:
> Hello gromacs users,
>
>
> I am facing a particular problem in the preparation of my
> protein.I have a NMR derived structure with hydrogens. To
> prepare my
I apology for the incorrect spelling of your name ...
I have an automatic reply format which sometimes does weird stuff ...
Sorry Prasenjit, really.
Regards
andrea
andrea spitaleri wrote:
> HI Pkmukher,
> I use to use opls for nmr structures in order to keep the all-hydrogen in the
>
nts? is it true this value or is it pbc artefact?
Thanks in advance
Regards,
and
ps. gmx3-3-1 compiled on suse-10.2 gcc-v 4.1.2
--
-------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (I
nm.
Any clue?
thanks again
Regards
andrea
andrea spitaleri wrote:
> Hi there,
> I have a complex protein-peptide in a box 6.5 6.5 6.5 with a starting
> periodic image of 3.0 nm,
> using PME and rlist=rvdw=rcoulomb=0.9.
> Now, I use to check the pi dist during my simulation in ord
weird
behaviour. Besides this,
it sounds very strange that the minimum distance goes from 3.0 nm to 0.17 nm
and then up to 3.0 in 2
ps ...
Therefore vmd and energy profile seem to be consistent with a proper simulation
(till now ..) :)
Thanks,
Regards
andrea
Miguel Machuqueiro wrote:
> At 08:00 AM 6
problem,
Regards
andrea
Yang Ye wrote:
> On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote:
>> At 08:00 AM 6/12/2007, you wrote:
>>> Hi again,
>>> since I did not get answer I double checked my trr file. In case I
>>> calculate the minimum distance of
>>>
erines).
Is there someone that could help me on this topic?
Thanks in advance
Andrea
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Please search the archive at http://www.gromacs.org/search before p
, but it asks me however for a group for the LSfitting..could
someone explain me this behaviour?
Is my procedure correct for my purpose? Is normal that g_cluster does
not accept the -fit option?
Thanks
Andrea
--
¯¯¯¯
Andrea Carotti
Dipartimento di Chimica e Tecnologia del
as imaging that it should have 2200 rows and 33
columns, am I wrong?
The second question is something that is already been asked before..it
could be usefull to obtain the matrix 2200 x 33 in a human readable
file. Is it possible without hacking the code? Perhaps using external
scripts?
Thanks a lot ag
umber of atoms (same
structure).
During the calculation i can see that it is creating the 2200x33 matrix,
but on the rmsd.xvg i find only two columns. From the xpm and dat files
i can't extract the matrix (i don't know) to a text file.
I hope this could clarify better m
-f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin
I obtain a rmsd.xvg with 2 columns. So, which is the meaning of that value? a
mean of all the rmsd calculated for that frame in respect to the other 33 refs?
Thanks
Andrea
--
Andrea Carotti
Dipartimento di Chimica e Te
> So does the -Rmat option not produce a human-readable text file?
Hi, unfortunately I can't see this option in g_rms.
I'm using the v 3.3.1 and also on the reference page online there is not
-Rmat. Am i missing something?
Thanks
Andrea
a step by step guru guide...
Thanks
Andrea
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