[gmx-users] (no subject)

[zaved]

Hii Everyone

I had performed a 100ns protein-ligand (docked complex) simulation with
gromacs 5.1.4.

The ligand in my case is hydrogen peroxide.

I have removed the PBC effect and centered the protein.

I have used the following commands:

gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc

gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc

I am analyzing the average distance between the protein and the ligand. I
am getting a value of 3.2nm which is too high.

Also in the out_1.xtc, after 10ns itself the ligand is moving all around
the protein.

Unable to understand why its happening!!

Please suggest.

Thank You

Regards

Z. Hazarika
Research Scholar
Tezpur University
Tezpur, India


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[gmx-users] positioning molecule at desired location

[Alex Mathew]

Dear all,

I want to keep a water molecule at a particular position of a protein
channel. I need to pull this across the channel and observe the energy
diagram by PMF. can anyone tell me how I can keep water molecules at a
particular position.

thank you.
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Re: [gmx-users] npt simulation error

[Mohammad Zahidul Hossain Khan]

; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r= 4


On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul  wrote:

>
>
> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> Dear Sir
>>
>> I am trying to simulate protein_ligand complex using epsilon = 4 and it is
>> giving the below error
>>
>>
> What is epsilon = 4?
>
> *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off
>> out of the domain decomposition cell of their charge group in dimension x*
>>
>> I have no idea how to solve this problem
>>
>>
> Have you Googled it, or gone to the GROMACS error page, where lots of
> advice lives? ;)
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
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>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] npt simulation error

[Justin Lemkul]

On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:

Dear Sir

I am trying to simulate protein_ligand complex using epsilon = 4 and it is
giving the below error



What is epsilon = 4?


*2 particles communicated to PME rank 4 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x*

I have no idea how to solve this problem



Have you Googled it, or gone to the GROMACS error page, where lots of advice 
lives? ;)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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[gmx-users] npt simulation error

[Mohammad Zahidul Hossain Khan]

Dear Sir

I am trying to simulate protein_ligand complex using epsilon = 4 and it is
giving the below error

*2 particles communicated to PME rank 4 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x*

I have no idea how to solve this problem
-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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[gmx-users] Doing restart

[‪farial tavakoli‬ ‪]

#yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted 
{margin-left:0 !important;border-left:1px #715FFA solid 
!important;padding-left:1ex !important;background-color:white;} Dear gmx users
I stoped my md simulation and now i want to restart it. 
I use gromacs 2016.3  and issued this command to perform md:Gmx grompp -f 
md.mdp -c npt.gro -t npt.cpt -p topol.tpr -n index.ndx -o md_0_1.tprGmx mdrun 
-deffnm md_0_1
To restart simulation i issuedGmx mdrun -s md_0_1.tpr  -cpi md_0_1.cpt 
-appendBut faced to an error:
Fatal error:
File appending requested, but 2 of the 3 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If the files are not available, you
can add the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead.

i refered to google but i couldnt understand well what should i type exactly. 
would you please help me to restart my md simulation?
Thanks in advanceFarial


Sent from Yahoo Mail for iPhone
 
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Re: [gmx-users] how to make molecular model with both ion channel and lipid bilayer?

[h . alizadeh]

Charmm-gui.org could help you.
Bests,
Hadi
On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong"  wrote:
Dear all,

I am trying to make a model of ion channel with cell membrane. Is there a 
specific software to make this? I mean just the coordination file. VMD can 
generate the membrane automatically, I can find the 'pdb' files of ion 
channels, but I have no idea how to combine them.

Thanks all,
Tong
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[gmx-users] how to make molecular model with both ion channel and lipid bilayer?

[Li, Tong]

Dear all,

I am trying to make a model of ion channel with cell membrane. Is there a 
specific software to make this? I mean just the coordination file. VMD can 
generate the membrane automatically, I can find the 'pdb' files of ion 
channels, but I have no idea how to combine them.

Thanks all,
Tong
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[gmx-users] (Don't know if mail worked last time)Drift with groups+tabulated potential.

[sperez14]

Dear GROMACS Community, 

First of all, if someone got this email twice, I am sorry. It is my
first post and I was not sure if it worked.  

I am trying to do a simulation using a tabulated potential which forces
me to use the group cut-off. I get a drift in the conserved quantity of
-600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
and a Na+ ion. I imagine that eventhough it will soon be deprecated the
group cutoff scheme still works correctly. I have tryed to change the
parameters without success and in any case the ones I use seem
reasonable (in my experience using other programs). The rdfs of the
system look normal so I ruled out topology problems.  

It seems that the problem is in the group cut-off since
when I change the tabulated potential for a regular vdw the problem
persists. I have followed the instructions of: 

http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf 

to implement the tabulated potentials. 

Is this the kind of energy drift acceptable? I have pasted a copy .mdp  

Thanks for your help, 

Sergio Perez-Conesa 

integrator = md 
dt = 0.001 
nsteps = 10 
init-step = 0 
cutoff-scheme = group 
nst-list = 1 
verlet-buffer-tolerance = 0.0005 
ns-type = grid 
rlist = 1.3 
pbc = xyz 
coulombtype = PME-switch 
rcoulomb = 1. 
rcoulomb-switch = 0.95 
pme-order = 4 
fourierspacing = 0.1 
ewald-rtol = 1.e-5 
vdwtype = user 
rvdw = 1.0 
DispCorr = No 
tcoupl = v-rescale 
tc-grps = System 
;nsttcouple = 1 
tau-t = ref-t = 300.0 
constraints = all-angles 
constraint-algorithm = LINCS 
lincs_iter = 1 
lincs_order = 4 
energygrps = NA OW 
energygrp_table = NA OW 
comm-mode = linear
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Re: [gmx-users] Fwd:

[Justin Lemkul]

On 8/15/17 1:52 AM, saranya wrote:

Hi,
I have done protein-drug simulations for 100ns. While calculating the hydrogen
bond between the protein-drug complex I am getting only 2 hydrogen bonds.
The number of H-bond formation is very low I have a question about is there
any influence of the drug in my protein?
To answer that, you need to do simulations of the apo protein and 
compare whatever relevant structural metrics there are (not H-bonds, as 
these tell you about the ligand-protein interactions but nothing about 
the impact on the protein structure).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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