Dear Mark, & Chris,
Thanks for your useful suggestions.
Yes Mark define = -DFLEXIBLE is the only difference in both the cases.
Actually in my previous post I have pasted only small section of tip4p.itp
file,(sorry if it created unnecessary confusions/doubt). This time I am
pasting full tip4p.it
Dear Chris,
Thanks for your help.
I have also tried the "comm_grps = System" option, and did energy
minimization but after that also water molecular looked like the previous
case (Figure-B, in my previous post).
Regards,
Alok
> >Dear All,
> >
> >I am doing the simulation of POPE lipid + Prote
Sorry again,
I just checked in case of TIP4P water molecules there is separate section
[ constraints ] which is used if we do not use FLEXIBLE water. It does
not uses SETTLE algorithm for constraining water molecules (correct me if
I am wrong). Sorry for my previous mail.
Regards,
Alok
> Dea
Dear Mark,
Thanks a lot for your reply.
Default was 1.6 angstrom and when I change gradually till 2.5 angstrom then
structure looks similar to original structure.
I have again checked in my top and mdp files for include statement.
I have define = -DFLEXIBLE in my mdp file
in my top file I have
Sorry for wrong link in my previous mail.
Dear Mark & Chris,
Thanks a lot for your help.
As both of you suggested I have increased the tolerance limit of the bond
(using VMD, as described by Chris), after increasing the Dynamic bond
length, the structure looks fine. So it means that during minim
Hello Huey Ling,
Use different chain identifiers for different peptides.
Then pdb2gmx will not create any bond between them.
Regards,
Alok
> Hi All,
>
>I am trying to put 2 identical peptide chains in a simulation box.
> However, gromacs tends to see both separate peptide chains as one.
>
hello chris,
thnks for your mail.So I just want to summarize our discusion
over the last few mails...please tell me if i am correct.
"When using OPLS-AA force field for simulation in GROMACS,it's correct to
get a 14 energy term (Scaled) in addition to the RB potential".
Ok so if
hello gmx users,
First of all thanks to Chris for his response to my
previous mail.But I still have a doubt regarding RB
potential which I would like to get clarified about.
I would be very thankfull if you can go through my
post (patiently) and comment on it.
_
Thanks David for your reply, I have a another doubt on OPLS force field
regarding 1-4 interaction.
In manual (chapter 4 page no 62) it was written The use of RB potential
implies exclusion of LJ interaction between first and the last atom of the
dihedral (mean 1-4 interaction).So why I am getting
Dear All,
I have a basic question on Dihedral angle in OPLS-AA force field.
I read some of the papers related to development of OPLS force field where
they have different formula for calculating the torsion angle
I think that is Ryckaert-Bellemans function, but there is no separate term
for Impro
Dear All,
two days back I posted a question regarding mdrun-hole but my
problem has still not ben solved,so I am writing it again in more
elaborate form. I appreciate any comment on my procedure.
In sort my problem is, I am not getting any output from modified
mdrun_hole program.
Here ar
Thanks Florian,
As you have replied, Yes I had activated logging (that
means I had the molsurf_log option in "for_hole.mdp" file .
But it is not creating my specified log file and also the
normal *.log file in run.mdp file)
As you had suggested I just tried with
nstlog
Dear All,
This question is regarding the modified mdrun program i.e mdrun_hole that is
used for creating hole in the lipid bilayer to insert a protein into it.
When I am trying to run the following command:
mdrun_hole -v -hole -holep for_hole.mdp -s run.tpr -o run.trr -x run.xtc
-c after_run.gro
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