study adsorption kinetics from one simulation?
Millions of thanks in advance for any tips or guidance
>
>
> Best Regards,
> Nima Soltani
> --
> MSc. of Physical Chemistry
> Sharif University of Technology.
> =====
Hello dear GROMACS users
I have recently submitted a manuscript
about
studying interactions of peptide-surface system.
one of the referees has asked
that :
"
"For the adsorption of the peptide on Au(111) in Figure 3 it seems that
there is a dynamic equilibrium between two
cture look likes this
:https://app.box.com/s/e6b87ar9j75q227qe6sx1udeyqdszgdl
Is there any way to correct those anomalies that can be observed in the
peptide's backbone?
thanks in advance for any help or guidance
Best Regards,
Nima Soltani
-
Justin Lemkul <jalemkul@...> writes:
>
>
> On 12/27/15 6:48 PM, Nima Soltani wrote:
> > Hi
> > I have performed principal component analysis by using g_covar module of
> > Gromacs 5.0 (Peptide's backbone atoms were selected both for least square
> >
cture look likes this :
https://app.box.com/s/e6b87ar9j75q227qe6sx1udeyqdszgdl
Is there any way to correct those artifices that can be observed in the
peptide backbone?
thanks in advance for any help or guidance
Best Regards,
Nima Soltani
-
Nima Soltani <nima.slt@...> writes:
> I really appreciate your time that you spend helping me Justin
> the starting structure looks like this:
> https://www.dropbox.com/l/qGSSN0MRJKUtJronECThnn
> and the topology of the *metal* is:
> https://www.dropbox.com/l/c0Cp7RUeua
Justin Lemkul <jalemkul@...> writes:
>
>
> On 9/1/15 10:29 PM, Nima Soltani wrote:
> > Nima Soltani ...> writes:
> >
> >>
> >> Thank you for your kind help dear Justin
> >> this is link of one of the pdb files that has been generated af
Justin Lemkul <jalemkul@...> writes:
>
>
> On 9/2/15 11:59 AM, Nima Soltani wrote:
> > Justin Lemkul ...> writes:
> >
> >>
> >>
> >> On 9/1/15 10:29 PM, Nima Soltani wrote:
> >>> Nima Soltani ...> writes:
> >>&g
Justin Lemkul <jalemkul@...> writes:
>
>
> On 9/1/15 9:40 AM, Nima Soltani wrote:
> > Hi everyone
> > I am simulating the interactions between a small peptide and different
> > metallic surfaces solvated in TIP3P water.
> > So far i have simulated 3
Thank you for your kind help dear Justin
this is link of one of the pdb files that has been generated after Blow up
by Gromacs:
https://www.dropbox.com/s/e3h05hohwp1va7p/step2170066b.pdb?dl=0
What other types of information do I need to provide?
Best Regards,
Nima Soltani
Justin Lemkul <jalemkul@...> writes:
>
>
> On 9/1/15 9:40 AM, Nima Soltani wrote:
> > Hi everyone
> > I am simulating the interactions between a small peptide and different
> > metallic surfaces solvated in TIP3P water.
> > So far i have simulated 3
Nima Soltani <nima.slt@...> writes:
>
> Thank you for your kind help dear Justin
> this is link of one of the pdb files that has been generated after Blow up
> by Gromacs:
> https://www.dropbox.com/s/e3h05hohwp1va7p/step2170066b.pdb?dl=0
> What other types of informat
---
Thanks in advance for any suggestions / assistance
Best Regards,
Nima Soltani
--
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology
-Nima Soltani
Grad. student of physical chemistry
Sharif Univ. of Tech.
Dr Anthony Nash
Department of Chemistry
University College London
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* Can't
Regards,
Nima Soltani
--
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
=
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org
you must supply an index file to the '-n' option
of grompp.
Could anybody tell me what's wrong with the COM pulling code I modified?
Best Regards,
Nima Soltani
--
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif
-011-090-4495
Fax: +39-011-090-4499
E-mail: annalisa.cardellini@...
SMaLL: http://www.polito.it/small
Best Regards
Nima Soltani
Graduate student
Sharif University of Technology
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Gromacs Users mailing list
* Please search the archive at
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, utilizing mgx make_ndx
command at previous step
Any advice or guidance would be greatly appreciated
Best Regards,
Nima Soltani
--
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology
/gmxpreprocess/readpull.c,
line: 257
Fatal error:
Group pull_group1 required by grompp was undefined.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Best Regards,
Nima Soltani
suppose that negative Chlorine ions should be
away from each other (same charge) and close to protein which has positive
charge. which is not!
is my simulation is incorrect?
if not what cause this seemingly strange thing to happen?
Thanks in advance for any guidance
Best Regards,
Nima Soltani
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