I want to run a simulation of cyclohexane in deuterated chloroform.
I was able to run a sim of cyclohexane in regular chloroform, but unable to
find how to make a solvent deuterated. I know that pdb2gmx has a -heavyh
and -deuterate option, would I do it this way? It isn't a protein and would
assum
Dear Gigo:
that's a good comprehensive testing and report. Please let us know what you
find out from those authors.
Their paper was short on methods (unless I missed it... I didn't check for any
SI), so perhaps they did something
non-standard and didn't report it.
I think at this point it is a
Hi all users,
Is it possible to add hydrogens to some of the selected atoms in the system
using pdb2gmx?
With best regards,
Naser
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* Please sear
Dear Chris,
I am really grateful for your help. This is what I did, with additional
LJ terms on LP1 and LP2 of tip5p:
- 5000 steps of steepest descent with positions restraints on protein
and flexible water (flexibility like in tip4p),
- 5000 steps of steep, no restraints, flexible water,
- 500
I see,
Thank you for the information Justin.
On Sep 28, 2013, at 2:57 PM, Justin Lemkul wrote:
>
>
> On 9/28/13 2:52 PM, Xu Dong Huang wrote:
>> Justin,
>>
>> I see. Is there a way to *stitch* the two files together so I can continue
>> onto a NPT run?
>>
>
> Appending is the default beh
On 9/28/13 2:52 PM, Xu Dong Huang wrote:
Justin,
I see. Is there a way to *stitch* the two files together so I can continue onto
a NPT run?
Appending is the default behavior of mdrun, if invoked properly and the files
haven't been messed with. If not, trjcat appends trajectories and enec
Justin,
I see. Is there a way to *stitch* the two files together so I can continue onto
a NPT run?
On Sep 28, 2013, at 2:49 PM, Justin Lemkul wrote:
>
>
> On 9/28/13 2:46 PM, Xu Dong Huang wrote:
>> Hello gromacs users,
>>
>> I restarted my run due to power failure using mdrun -v -s .t
On 9/28/13 2:46 PM, Xu Dong Huang wrote:
Hello gromacs users,
I restarted my run due to power failure using mdrun -v -s .tpr -cpi
.cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make
it so it continues to update the original .xtc and .tpr files?
If you're ge
Hello gromacs users,
I restarted my run due to power failure using mdrun -v -s .tpr -cpi
.cpt, but the output files generating -s.gro , -s.tpr -s.xtc, how do I make
it so it continues to update the original .xtc and .tpr files?
Thanks,
Xu Huang
Research Assistant
Chemical & Biochemica
On 9/28/13 11:20 AM, bipin singh wrote:
Hi all,
I want to put off constraint between some bonds in my system based on their
atom numbers but the .gro file and .top file atom numbers do not match,
because I used .pdb file to generate this .top file using pdb2gmx. (the top
files contains the ato
Dear Gigo:
everything that I suggested was just ways that you might get a system without
bad contacts to
start your simulation with the proper (standard) tip5p model and oplsaa. I
expected that combination
to work together since they came out of the same lab, but looking at the
initial tip5p pa
Hi all,
I want to put off constraint between some bonds in my system based on their
atom numbers but the .gro file and .top file atom numbers do not match,
because I used .pdb file to generate this .top file using pdb2gmx. (the top
files contains the atom numbers based on this initial input .pdb f
On 09/28/2013 09:42 AM, rajat desikan wrote:
Hi,
I am not sure, but try resname SOL or something similar. Also, your first
line has waterO and second line has water0.
Hi Rajat:
thanks a lot for such kind and helpful comments. It works now. I run it
by command:
g_select_mpi -f ../md_pbc_cen
Hi,
I am not sure, but try resname SOL or something similar. Also, your first
line has waterO and second line has water0.
On Sat, Sep 28, 2013 at 1:00 PM, Albert wrote:
> Hello:
>
> I am trying to analyze the water density along Z direction of my protein.
> Here is my g_select command:
>
> g_s
Hello:
I am trying to analyze the water density along Z direction of my protein.
Here is my g_select command:
g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf
select.dat
and here is my select.dat:
waterO = water and name OW and z>30 and z<70;
close = water0 and within 0.4
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