Objet : Re: Re : [gmx-users] Re: Adding Ions
errabah fatima ezzahra wrote:
>
> *I am trying to do a Short position restrained simulation so i wrote * grompp
> -f pr.mdp -c system.gro -p file.top -o file.tpr , i added the NA+ to the
> pr.mdp file
> here the p
??
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Mercredi 13 Juillet 2011 14h42
Objet : Re: Re : [gmx-users] Re: Adding Ions
errabah fatima ezzahra wrote:
>
> *I am trying to do a Short position restrained simulation so i wrote * grompp
n.
i dont have an indexfile ?
FZ
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Mercredi 13 Juillet 2011 14h11
Objet : [gmx-users] Re: Adding Ions
errabah fatima ezzahra wrote:
> Hi Justin
>
> when i seperated the NA+ and 6
Hi Justin
when i seperated the NA+ and 6 i got this error
NOTE 1 [file em.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rcoulomb.
NOTE 2 [file em.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to
Objet : Re: Re : [gmx-users] Adding Ions
Justin A. Lemkul wrote:
>
>
> errabah fatima ezzahra wrote:
>> i added the NA using the genion
>> *
>>
>> genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA to
>>the topology file ,
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Mercredi 13 Juillet 2011 13h05
Objet : Re: [gmx-users] Adding Ions
errabah fatima ezzahra wrote:
>
> Hi All,
>
>
> I have a peptide that has three positive charged amino acids (LYS)
Hi All,
I have a peptide that has three positive charged amino acids (LYS) and four
negative charged amino acids (GLU) consequently it is a negative peptide. is
that right
when i run gromacs simualtion grompp DOES NOT gave a warning:
System has non-zero total charge: -6 ( i have six peptides)
Objet : Re: Re : Re : Re : Re : Re : [gmx-users] Re: Hexamer problem/ The N and
C termini of peptides
errabah fatima ezzahra wrote:
> Hi All
>
> I am using course grained model where i have the whole glutamic acid as a
> sphere , and the other end is Lucine (hydrophobic) , do i n
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Jeudi 7 Juillet 2011 17h03
Objet : Re: Re : Re : Re : Re : [gmx-users] Re: Hexamer problem/ The N and C
termini of peptides
errabah fatima ezzahra wrote:
> Thank you so much for your h
: Re : Re : [gmx-users] Re: Hexamer problem/ The N and C termini
of peptides
errabah fatima ezzahra wrote:
> I am sorry to be asking you again but do you start with different velocities
> by changing the temperature that will lead to change in velocities, i ma new
> to Gromacs so i
zahra
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Jeudi 7 Juillet 2011 14h55
Objet : Re: Re : Re : [gmx-users] Re: Hexamer problem/ The N and C termini of
peptides
errabah fatima ezzahra wrote:
> *
>
> hello
> Does
errabah fatima ezzahra wrote:
> *
>
> hello
> Does anybody knows why The N and C termini of peptides can be neutralized
> before running simulation of peptides ?? i read this some where in a
> research paper , they dont say why but they do that using acetyl amine
> groops.
ezzahra
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Jeudi 7 Juillet 2011 9h33
Objet : Re: Re : [gmx-users] Re: Hexamer problem/ high and low salt solutions.
errabah fatima ezzahra wrote:
> Hi
everybody
>
> i did Again run the simulation for 2000ns and the
.
please any suggestion will be appreciated
thank you
fatima-ezzahra
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Mercredi 6 Juillet 2011 10h01
Objet : [gmx-users] Re: Hexamer problem
errabah fatima ezzahra wrote:
> Hi All;
>
>
>
> *De :* Justin A. Lemkul
> *À :* errabah fatima ezzahra ; Discussion list for GROMACS
> users
> *Envoyé le :* Mardi 5 Juillet 2011 15h06
> *Objet :* Re: [gmx-users] Hexamer problem
>
>
>
> errabah fatima ezzahra wrote:
> >
>
thanks for your help
fatima-ezzahra
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Mardi 5 Juillet 2011 15h35
Objet : Re: Re : [gmx-users] Hexamer problem
errabah fatima ezzahra wrote:
> Hi justin
>
> Thank you so much
I will really appreciate any help of suggestions.I am doing simulation of six
monomers of identical helical peptide. the experiment literature say that the
peptides in a aqueous solution should form a hexamer. so i have done
simulations for the six peptides under normal conditions with T of
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