used.
Thank you very much for your help.
On Mon, Jan 22, 2018 at 1:05 PM, Sailesh Bataju <thela...@gmail.com> wrote:
> Hi,
>
> I have been trying to simulate isobutane in urea as a solvent. I have made
> myself urea.itp and urea.gro file for charmm36 forcefield under
> equ
"
#ifdef POSRES
#include "posre_urea.itp"
#endif
; Include topology for ions
#include "charmm36.ff/ions.itp"
[ system ]
; Name
Isobutane in Urea
[ molecules ]
; Compound#mols
Alkane_chain_A 2
Urea 841
Any idea to solve this problem.
Thank you for your time
it produce different results (relative to pull-geometry =
distance)? I've no idea what is the best to be done for the last 4 frames.
Considering the time I spent for the simulation, please introduce me the
best alternative way to go ahead.
Thank You
Sailesh Bataju
--
Self-reliant is the great
"
[ system ]
; Name
ALKANE ISOMER OF N-BUTANE
[ molecules ]
; Compound#mols
Alkane_chain_A 1
I think [bonds], [pairs],etc section should be automatically filled
up. Did I do something wrong?
Thank you very much.
On Wed, May 24, 2017 at 8:51 AM, Sailesh Bataju <thela...@gmail
>>* Making bonds...
*>>* Warning: Short Bond (5-1 = 0.025 nm)
*>>* Warning: Long Bond (5-6 = 0.99084 nm)
*>>* Warning: Long Bond (1-2 = 0.944378 nm)
*>>* Warning: Long Bond (1-3 = 0.895661 nm)
*>>* Warning: Long Bond (1-4 = 0.866986 nm)
*>>* Warning: Long Bond (7-8 = 0.502204 nm)
*>>* Warning:
>The easiest thing to do
>(solving this issue and #1) is to create an isobutane .rtp entry and have
>pdb2gmx do all the work for you. It's very simple to do.
> -Justin
Thank you sir, I've exactly followed your steps. I've created
isobutane.rtp file and modified residuetypes.dat file by adding
compound
>in
>existing force fields and should have parameters published and validated for
>any
>of the major all-atom force fields. I know it's in CHARMM, and certainly
>others.
>Justin
On Fri, May 19, 2017 at 6:07 PM, Sailesh Bataju <thela...@gmail.com> wrote:
>
Hi Sir,
You mean like choosing OPLS forcefield for all-atom model would be moer
appropriate for me?
Thank you.
On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju <thela...@gmail.com> wrote:
> Hi Sir/Ma'am,
>
> I've finally created parameter file of isobutane using gromos54a7
>
Hi Sir/Ma'am,
I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefield, instead I used FTFE - CTFE - FTFE and
Hi,
I need to search parameters like bond length, bond angle, atomic charge,
dihedral angle, improper dihedral angle and Lennard Jones potential
parameters like C6 and C12 of isobutane molecule. I've searched those
parameters in ffbonded.itp and ffnonbonded.itp files inside gromos54a7
forcefield.
Hi,
I've been following KAlP15 in DPPC tutorial successfully but now I stuck in
the last Analysis section. I googled the problem there's nothing out. The
question is so simple it's just a misunderstanding. In the 2nd part Density
of the Membrane the code is
# gmx make_ndx -f md_0_1.tpr -o
Hi,
Thank you sir for your immediate response. So is there any way that I
can fix this problem expect not renaming file at different stages. If
there is, help me with the command.
Thank you for your consideration.
--
Self-reliant is the great potential for success.
--
Gromacs Users mailing
Hi,
I'm following tutorial of "Lysozyme in Water" and playing with mdrun,
restarted several times as an experiment and got confusion whether the
restart process may have effect on subsequent process.
Here is what I did.
Suppose nvt.tpr file is generated then
1st: gmx mdrun -deffnm nvt -v -maxh
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