water in your system (or if have more water than you want
>> in your final structure), go back to step 3 and continue removing.
>>
>>
>> You should not remove a large amount of molecules in a single step or this
>> can lead to some artificial structures. A
total charge of each
> molecule be neutral. But we don't know enough about what you're doing yet.
>
> Mark
>
> On Thu, 5 Dec 2019 at 23:34, SAKO MIRZAIE wrote:
>
>> Dear Justin,
>>
>> Thank you for your answer. when I use just one chain of polymer with the
>&g
ec 3, 2019 at 4:04 PM Justin Lemkul wrote:
>
>
> On 12/3/19 3:59 PM, SAKO MIRZAIE wrote:
> > Hi All,
> > I did some MD studies on a protein: polymer system. After running
> grompp,
> > it said, "the total charge is not an integer". the total charge
Hi All,
I did some MD studies on a protein: polymer system. After running grompp,
it said, "the total charge is not an integer". the total charge is -0.00465.
Can I continue the MD by adding -maxwarn flag? or it will be a problem and
I will get unrealistic results?
Best,
--
>
> regards
>
> Andre
>
> On Mon, Dec 2, 2019 at 2:54 AM SAKO MIRZAIE
> wrote:
>
>> Dear André,
>>
>> Thank you for your response.
>> Could you send me such a script?
>>
>> On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura
>> wrote
Dear André,
Thank you for your response.
Could you send me such a script?
Best
--
***
Sako
On Mon, Dec 2, 2019 at 12:54 AM SAKO MIRZAIE wrote:
> Dear André,
>
> Thank you for your response.
> Could you send me such a script?
>
> O
of the files as well).
>
> Andre
>
> On Sun, Dec 1, 2019 at 8:03 PM SAKO MIRZAIE
> wrote:
>
>> Hi All,
>>
>> I want to simulate a polymer: protein system in a way that water solvent
>> will evaporated gradually. How should I do that?
Hi All,
I want to simulate a polymer: protein system in a way that water solvent
will evaporated gradually. How should I do that? What parameters are needed
to be included in the mdp file.
Best
--
***
Sako
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Thank you. is there any tutorial to do that? I know I should do it with
Quantum mechanics (e.g. gaussian package), but I don't know how.
best regards,
On Mon, Oct 17, 2016 at 1:22 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 10/15/16 1:35 PM, SAKO MIRZAIE wrote:
>
&g
,
--
***
Sako Mirzaie
PhD in biochemistry, Assistant Professor, science faculty, Islamic Azad
university of
Sanandaj, Sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie
http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie
http://scholar.google.com/citations?user=viwZvVAJ=en
a, PA 19104
>
> Voice: (662) 617-2267
> E-mail: cj...@drexel.edu
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--
*******
Sako Mirzaie
PhD in biochemistry, Assistant Professor, science faculty, Islamic Azad
university of
Sanandaj, Sana
May I upload my input and output files? solving this problem is really
critical for me.
thanks,
On 8/24/16, SAKO MIRZAIE <sako.bioc...@gmail.com> wrote:
> I have added the following residue to rtp:
> [ PES ]
> [ atoms ]
>H1HO 0.405002 1
>O1
0.0357007
OS OH-0.6033018
HS HO 0.4050009
[ bonds ]
O1C1
C1C2
C1H1
C1H2
C2H3
C2H4
C2OS
OSH5
-C2O1
I also tried with gromacs 5, but I got the same error.
On 8/24/16, SAKO MIRZAIE
is unlikely to be called em_out.log, which might be a file you wrote with
> mdrun?
>
> Mark
>
> On Wed, Aug 24, 2016 at 12:59 AM SAKO MIRZAIE <sako.bioc...@gmail.com>
> wrote:
>
>> I am using gromacs 4.5. my grompp input files are just topology and a
>> gro file. nei
> like the whole grompp output (or at least error message without copy-paste
> typos), and your GROMACS version. Probably you've mistakenly used some part
> of the .rtp format in one of your .itp files.
>
> Mark
>
> On Wed, Aug 24, 2016 at 12:10 AM SAKO MIRZAIE <sako.bioc...@
don't
know what does it mean. any help is appreciated.
best regards
--
*******
Sako Mirzaie
PhD in biochemistry, Assistant Professor, science faculty, Azad university of
Sanandaj, Sanandaj, Iran
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-- Forwarded message --
From: SAKO MIRZAIE <sako.bioc...@gmail.com>
Date: Fri, 3 Jun 2016 20:04:49 +0430
Subject: top parameters for pluronic f127
To: gromacs.org_gmx-users@maillist.sys.kth.se
Dear All,
I am trying to convert my mol2 file to amber99sb itp to do MD by
g
simulate it in MD by gromacs? do polymers have some
tricks?
the molecular structure of f127 is: A99B67A99
where
A: ethylene oxide
B: propylene oxide
best regards,
--
***
sako mirzaie
PhD in biochemistry
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simulate it in MD by gromacs? do polymers have some
tricks?
the molecular structure of f127 is: A99B67A99
where
A: ethylene oxide
B: propylene oxide
best regards,
--
***
sako mirzaie
PhD in biochemistry
simulate it in MD by gromacs? do polymers have some
tricks?
the molecular structure of f127 is: A99B67A99
where
A: ethylene oxide
B: propylene oxide
best regards,
--
***
sako mirzaie
PhD in biochemistry
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Gromacs Users mailing list
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and also this one:
http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/
On 3/31/16, SAKO MIRZAIE <sako.bioc...@gmail.com> wrote:
> hi
> you can do MD simulation and compute free energy of folding,
> individually. for detect the folding frame or structure, use h
<tusharranjanmohar...@gmail.com> wrote:
> Hi SAKO MIRZAIE,
> Thanks for your reply. But how can we calculate difference in folding free
> energy by doing 2 separate simulations? Please clarify (at least give some
> hints or references).
>
> Thanks a lot.
>
> "A society
t; https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
>
--
***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj,
hive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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visit
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***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.
Hi,
I have a server with suse enterprise linux, two zeon cpu (2630) and a
gpu (gtx titan x). I tried to install gromacs 5, but the following
error appeared:
cannot find AVX compiler flag,
how can I fix the error?
best regards,
--
***
sako mirzaie
Dear all,
I just trying to add two itp files including NADP.itp and
ligand.itp in my topology file by add #include NADP.itp
#include ligand.itp after force filed amber99sb. but the following
error appears:
' [ atomtypes ]'
invalid order for directive atomtypes
.
.
.
when I delete the #include
: optional Cable Manage ( DEEP COOL Pro Series )
best regards,
--
***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie
http://www.iausdj.ac.ir/en
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