the topol.top adds CL at the end under [molecules] but when I
try to minimize the geometry using the new solvate.gro file the error as
given as
ERROR 1 [file topol.top, line 37]:
No such moleculetype CL
I do not understand how I can rectify the problem. Can someone help?
*Thank you*
*Gangotri
*
On Mon, Sep 18, 2017 at 7:53 PM, Justin Lemkul wrote:
>
>
> On 9/18/17 4:18 PM, gangotri dey wrote:
>
>> Hello!
>>
>> I would save it in vmd all at once but I would like to ideally save it in
>> separate files. Also, the trajconv statement did not work.
>&g
I hope your gromacs is compiled in a parallel cluster for you to use
gmx_mpi.
*Thank you*
*Gangotri *
On Tue, Sep 19, 2017 at 11:06 AM, K. Subashini
wrote:
> Hi gromacs users,
>
>
> I am using version 5.1.4
>
>
> How to use gmx_mpi?
>
>
> I got the following error message
>
>
> Executable:
xtc file.
> right click on to it and save coordinate. File type. gro.
> or
> trajconv -f xxx.trr or xtc -s xxx.tpr -o xxx.gro
>
> RC Dash,
>
>
> On Mon, Sep 18, 2017 at 2:42 PM, gangotri dey
> wrote:
>
>> Dear all,
>>
>> I would like to transform my
Dear all,
I would like to transform my trajectory file n.trr or n.xtc to n.gro after
my production run. I have used trjcat and trjconv to transform it using the
index file. But in both the cases, it says "Can not write a gro file
without atom names". How can I transform it please?
*Thank you*
Dear all,
I have a simulation that I ran for 5 ns. I have saved after every 0.1 ps. I
would like to extract the structure after every 1 ns. Is there any easy
way to do it in gromacs?
*Thank you*
*Gangotri Dey*
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this done as desired.
If the question and the problem are not very clear, please let me know. I
will try to reframe my words.
Looking forward to a healthy discussion.
Thank you
G.
*Thank you*
*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
you*
*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
On Mon, Aug 7, 2017 at 5:04 PM, Mark Abraham
wrote:
> Hi,
>
> Are you trying to implement a model that you know i
Dear all,
I am working with MnO2 surface and I would like to solvate the surface only
in the z-direction. How best can I do it, please?
*Thank you*
*Gangotri Dey*
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gen_vel = yes ; assign velocities from Maxwell
distribution
gen_temp= 300 ; temperature for Maxwell distribution
gen_seed= 18; generate a random seed
*Thank you*
*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
distribution
gen_temp= 300 ; temperature for Maxwell distribution
gen_seed= 18; generate a random seed
*Thank you*
*Gangotri Dey*
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Thank you for the kind reply. I will compute and update in the post.
*Thank you*
*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
On Fri, Aug 4, 2017 at 10:31 AM, Mark
-84.24 0 100
702698716712 150.3766 0 100
695691692702 1 -166.8294 0 100
My .mdp file is similar to the one used in the Bevan lab tutorial online.
*Thank you*
*Gangotri Dey*
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*Gangotri Dey*
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Hey!
You might want to constrain the bond between the 2 protein chains.
G
*Thank you*
*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
On Fri, Jul 21, 2017 at 8:56 AM
previous version in the mdp file.
However, the dihedral angles are changing and I am not sure how to restrain
them.
Is there any part that I am missing.
*Thank you*
*Gangotri Dey*
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