Dear all,
I am truing to do an MD simulation on dendrimeric structures. I can perform
all steps successfully, but I get a NOTE in all steps after Adding Ions as
follows:
NOTE 2 [file topol.top]:
The largest charge group contains 20 atoms.
Since atoms only see each other when the centers of
Hi all,
I have a solvent filled in a box of dimensions 12 12 12 (solv_large.gro).
I want to adjust the density of system to 824 kg/m3. But I want editconf to
just change the volume only by changing the z direction ? is that possible?
I did
ediftconf -f solv_large.gro -o solv_large_scaled.gro
let me modify my previous message: in the g_x2top command, not grompp :-)
On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar maryam.kow...@gmail.com
wrote:
Hi Mohammad,
Yes that's possible. You should just have the necessary files of your
desired forcefield(.atp,.itp,...), and put them in a
2015-08-09 18:25 GMT+01:00 Justin Lemkul jalem...@vt.edu:
Are you using some old version? Note that your cutoff setup is wrong for
CHARMM force fields.
Well, to be honest I do use quite and old version which is 4.6.7.
Yes I am aware of that I use wrong CHARMM force field cutoff setup and
2015-08-09 18:27 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com:
Justin's advice is true only if your water topology has a flexible
implementation. Check it
Yes, I do use flexible water and still this causes problem.
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Hi,
Justin's advice is true only if your water topology has a flexible
implementation. Check it.
Mark
On Sun, 9 Aug 2015 17:41 Dawid das add...@googlemail.com wrote:
Dear Justin,
I still have problems with performing l-bfgs minimization.
I use
constraints = none ; no
Hi,
As you have seen, if you have a periodic simulation volume dominated by
e.g. protein then the standard definition of concentration will not lead to
conditions analogous to e.g. an experiment with protein in a bulk solution.
Choose something that models the relevant aspects well, defend it
On 8/9/15 12:55 PM, Vy Phan wrote:
Dear Gromacs Users
I run membrane protein with DOPC lipip. Without protein, the
lipid-ions-water system can run energy minimization. But when I insert
protein in the center of that system (I removed the overlapping molecules),
but this system can not run. I
On 8/9/15 12:59 PM, mohammad r wrote:
Thank you MaryamI want to use this force field in the first step of generating
the topology file (pdb2gmx command in the force field shown after this
command). Is it possible? and unfortunately I don't know how to find the
necessary files of this force
I did a similar task. You should know the parameters and convert your files
format to gromacs format. A bit difficult but possible.
On Sun, Aug 9, 2015 at 9:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/9/15 12:59 PM, mohammad r wrote:
Thank you MaryamI want to use this force field in
Hi;
I want to use ff14SB Amberprotein force field. But it isn't included in the
gromacs force fields list.Is it possible to use this force field? How can I add
it in?Thank you, Mohammad.
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Hi Mohammad,
Yes that's possible. You should just have the necessary files of your
desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp
command just add -ff folder name. that's all! It will use your forcefield
instead of the present forcefields in gromacs.
Regards,
-Maryam
Hi,
That is unlikely to work for large changes in density, because bond lengths
get messed up too badly. Instead, you can use Berendsen pressure coupling
with a larger or smaller target pressure to slowly change the volume in an
actual simulation. Equilibrate thoroughly afterwards!
Mark
On Sun,
I hope speedy share is fine.
http://www.speedyshare.com/k2YEr/ribonucl-no-constr.tar.gz
2015-08-09 18:08 GMT+01:00 Justin Lemkul jalem...@vt.edu:
On 8/9/15 11:40 AM, Dawid das wrote:
Dear Justin,
I still have problems with performing l-bfgs minimization.
I use
constraints
Dear Justin,
I still have problems with performing l-bfgs minimization.
I use
constraints = none ; no constraints
define = -DFLEXIBLE
in my *mdp file and in *top file there is nothing related to constraints.
I still get this error that l-bfgs and constraints are
Dear Gromacs Users
I run membrane protein with DOPC lipip. Without protein, the
lipid-ions-water system can run energy minimization. But when I insert
protein in the center of that system (I removed the overlapping molecules),
but this system can not run. I always got this message. Actually, I do
You've *tried* to use flexible water. But does your water itp file *have* a
flexible implementation that your approach will trigger?
Mark
On Sun, 9 Aug 2015 19:42 Dawid das add...@googlemail.com wrote:
2015-08-09 18:27 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com:
Justin's advice is
You do not state your original density. But lets say you need to reduce volume
3% to get your correct density. Use:
ediftconf -f solv_large.gro -o solv_large_scaled.gro -scale 1 1 0.97
Just do a quick side calculation for what you need and substitute in for 0.97.
Dan
On Aug 9, 2015, at 4:18
Thank you MaryamI want to use this force field in the first step of generating
the topology file (pdb2gmx command in the force field shown after this
command). Is it possible? and unfortunately I don't know how to find the
necessary files of this force field. I searched a lot but I didn't
On 8/9/15 1:17 PM, Dawid das wrote:
I hope speedy share is fine.
http://www.speedyshare.com/k2YEr/ribonucl-no-constr.tar.gz
Works for me with the latest GROMACS. Are you using some old version? Note
that your cutoff setup is wrong for CHARMM force fields. See
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