Hi everyone,
I am looking for an Amber based force field for chloroform as a solvent to
use with Gromacs. I adopted GAFF ff from http://virtualchemistry.org.
The partial charge on chlorine and carbon which are +ve and -ve,
receptively, are a bit confusing. Since chlorine is more electronegative
t
Dear GROMACS users,
I am trying to simulate a triclinic crystal at the center with solvent on
either side in the z-direction and periodic x-y plane. The crystal box is
very skewed with one of the angles from the horizontal axis is 30 degrees.
I have first simulated it in the triclinic box but appa
Hi everyone,
I figured out the problem in my topology. One line which was supposed to be
commented was not.
Thanks
Lakshman
On Mon, Mar 18, 2019 at 3:18 PM Lakshman Ji Verma
wrote:
> Hi everyone,
>
> I am trying to simulate an organic molecule with chloroform as a solvent.
> I p
Hi everyone,
I am trying to simulate an organic molecule with chloroform as a solvent. I
prepared opls based topology for both the molecules from Ligpargen server.
The topology for chloroform works fine when I have only chloroform in the
system. I checked it against work done previously. However,
Thanks, Justin,
Is there any tool in Gromacs which can give the average box angles?
g_energy only give dimensions in terms matrix parameters but not in terms
of box angles.
Thanks
Lakshman
On Mon, Nov 19, 2018 at 5:53 PM Justin Lemkul wrote:
>
>
> On 11/19/18 5:42 PM, Lakshman Ji Ve
Lakshman
On Mon, Nov 19, 2018 at 5:53 PM Justin Lemkul wrote:
>
>
> On 11/19/18 5:42 PM, Lakshman Ji Verma wrote:
> > Hi all,
> >
> > I am trying to validate a force field (ff) for a crystal structure. I
> have
> > done isotropic NPT simulations without restra
Hi all,
I am trying to validate a force field (ff) for a crystal structure. I have
done isotropic NPT simulations without restrains.
I want to calculate the box length and angle (alpha, beta, gamma) to check
the validity of the ff. I found one similar thread but it doesn't answer
my question.
http
Hi everyone,
I am trying to simulate a crystal slab using 3dc Ewald correction and PBC
in xyz with dimensions 3.5nm*4.4nm*3.2nm and with the box length of more
than 3xZ in the z-direction with my slab in the center of the box, as
recommended in GROMACS manual. I am getting the following warning:
Hi Momin,
This won’t work unless you are simulating only single molecules i.e. only
unit cell with box parameters same as unit cell. Broken molecules will have
larger distances between atoms than actual bond length in a crystal
containing more than one unit cell, which will give error. So you need
gt; than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: non-global thermostatting (Justin Lemkul)
>2. potential energy (Mahboobeh Eslami)
>3. Re: zig-zag stacking (Dan Gil)
>4. Re: ndx file with frames (Dan Gil)
Adding on to Dan’s suggestions, you can create a box containing two unit
cell using editconf (translate one molecule accordingly) and then replicate
that box using genconf to get required confirmation.
Thanks!
Lakshman
On Tue, Jul 31, 2018 at 6:39 PM Dan Gil wrote:
> Hi,
>
> I haven't tried it,
Based on these figures it appears that bonds are breaking which means they
are not defined correctly in your topology file.
Based on my experience, you might want to look in your .rtp file and ZIF
gro/pdb file and check the sequence of the atoms. All three files must have
the same sequence of atoms
On Wed, Jul 25, 2018 at 8:32 AM Jordan Chapman
wrote:
> GROMACS users,
>
> I am attempting pre-processing of a metal organic framework (ZIF-8) in
> water, but I am running into trouble with energy minimization. I've added
> both bonded and nonbonded forcefield parameters for ZIF-8 into the AMBER0
Thanks Justin.
On Tue, May 29, 2018 at 11:09 AM, Justin Lemkul wrote:
>
>
> On 5/29/18 12:04 PM, Lakshman Ji Verma wrote:
>
>> Thanks Justin. A follow up question for my better understanding.
>>
>> Does it mean that with “periodic-molecules” False, the p
10:53 AM Justin Lemkul wrote:
>
>
> On 5/29/18 11:50 AM, Lakshman Ji Verma wrote:
> > What difference it will make I keep Periodic molecules option True or
> False?
> > I read the manual but couldn’t understand more than keeping it False will
> > be faster.
>
>
What difference it will make I keep Periodic molecules option True or False?
I read the manual but couldn’t understand more than keeping it False will
be faster.
Thanks!
Lakshman
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Do it multiple times by center the ligand first and then protein in the
other step,while using pbc. Use -pbc mol option in one of the step to get
the whole molecule.
Thanks
On Thu, Dec 28, 2017 at 6:26 AM Neha Gupta wrote:
> I gave
>
> gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 5.0 -
Thanks Justin
Regards,
Lakshman
On Thu, Jul 13, 2017 at 8:27 PM, Justin Lemkul wrote:
>
>
> On 7/13/17 10:37 AM, Lakshman Ji Verma wrote:
>
>> Dear all,
>>
>> I want to ramp down the restraint on the two molecules from 1000k to 0 on
>> some time interval so
Dear all,
I want to ramp down the restraint on the two molecules from 1000k to 0 on
some time interval so that restraint is removed gradually. My colleagues
said that it can be done with single md parameter file in LAMMPS and NAMD.
Can this be done using a single .mdp file in Gromacs too? Or I wi
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