[gmx-users] Scd

[m g]

Dear Justin,I want to obtain the error bar for deuterium order parameter (Scd). 
what command must i use for it?regards,Mr.Ganj
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[gmx-users] Error in number og H-bond

[asasa qsqs]

Dear Justin,I calculated the H-bond with g_hbond. I want to calculate the error 
of H-bond, what must i do?many thanks,Mrs. Mahdavi
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[gmx-users] forcefield parameter for bromide ion

[jagannath mondal]

Hi
  I need to do a simulation of protein in presence of LiBr salt solution.
However, I am not finding any force field parameters for bromide ion either
in charmm forcefields or amber forcefields. Can someone suggest a decent
source for bromide ion forcefield parameters that one could employ in
simulation involving protein.
Jagannath
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Re: [gmx-users] GPU installation of gromacs:Tesla K20c

[Peter Kroon]

1) put `source /usr/local/gromacs/bin/GMXRC` in your ~/.bashrc file.
2) Type `echo $PATH` and make sure you find your path to Gromacs in there.
3) try `gmx mdrun`. Im not sure whether that is already required for
Gromacs 5.0.5. Also, have a look in /usr/local/gromacs/bin to see
whether 'gmx', 'mdrun' and 'pdb2gmx' exist.

Peter

On 09/10/15 07:48, Nikhil Maroli wrote:
> Dear all,
> i have Tesla K20 GPU and ubuntu 15.04 and i installed cuda 7.5.after that i
> executed the following commands
>
> tar xfz gromacs-5.0.5.tar.gz
> cd gromacs-5.0.5
> mkdir build
> cd build
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> make
> make check
> sudo make install
> source /usr/local/gromacs/bin/GMXRC
>


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Re: [gmx-users] dihedral calculation

[Justin Lemkul]

On 10/9/15 6:06 PM, Parvez Mh wrote:

Dear all,

I want to measure dihedral angle of a particluar dihedral over all time
steps. I see in gromacs that g_angle can calculate the distribution of
dihedral but not the exact angle measurement. Is there any option in
gromacs to measure dihedral over the all time steps.



Option -ov does this.  Add -all if analyzing multiple dihedral simultaneously.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] dihedral calculation

[Parvez Mh]

Dear all,

I want to measure dihedral angle of a particluar dihedral over all time
steps. I see in gromacs that g_angle can calculate the distribution of
dihedral but not the exact angle measurement. Is there any option in
gromacs to measure dihedral over the all time steps.

Thanks
Masrul
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Re: [gmx-users] dihedral calculation

[Parvez Mh]

Thanks Dr. Lemkul

Regards
Masrul

On Fri, Oct 9, 2015 at 5:08 PM, Justin Lemkul  wrote:

>
>
> On 10/9/15 6:06 PM, Parvez Mh wrote:
>
>> Dear all,
>>
>> I want to measure dihedral angle of a particluar dihedral over all time
>> steps. I see in gromacs that g_angle can calculate the distribution of
>> dihedral but not the exact angle measurement. Is there any option in
>> gromacs to measure dihedral over the all time steps.
>>
>>
> Option -ov does this.  Add -all if analyzing multiple dihedral
> simultaneously.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Virtual sites error

[Timofey Tyugashev]

This looks very strange that from the whole assortment of the molecules 
in the force field only a humble methyl group in thymine lacks proper 
definition causes such an error.
Even nucleotides which I added myself to the force field files don't 
produce any errors
Is there any way to remedy this without significant hassle? What things 
are exactly lacking?

--

Message: 4
Date: Thu, 8 Oct 2015 11:15:17 +
From: Erik Marklund 
To: "gmx-us...@gromacs.org" 
Subject: Re: [gmx-users] Virtual sites error
Message-ID: <89ae0bec-6d9f-49a0-83e2-5ad8d7734...@chem.ox.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Unfortunately, the parameters required for certain virtual sites in nucleic 
acids are not define in the force field files that are shipped with Gromacs.

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ


On 7 Oct 2015, at 11:33, Timofey Tyugashev  wrote:

Trying to add hydrogen virtual sites to the model (using -vsites h option in 
pdb2gmx) results in a salvo of error messages when running grommp to create 
.tpr file after the solvation:

ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
  No default Constr. No Conn. types


ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
  No default Constr. No Conn. types

This lines in constraints section in the .itp file refer to pairs of two MCH3 
and one MC atoms, which should serve (the way I understand the situation) as 
replacement methyl group in thymine. There are several more pairs of same 
errors corresponding to different thymine methyl groups in the DNA strands.

Here is the relevant sections of the itp file for the first two errors:

[ constraints ]
;  aiaj functc0c1
2 3 2
  110   111 2
  110   112 2
  111   112 2

[ atoms ]

   110 CM321 DT C5110 0.0025 12.01   ; qtot -2.867
   111   MCH3321 DT   MC71111  0 7.517   ; qtot -2.867
   112   MCH3321 DT   MC72111  0 7.517   ; qtot -2.867
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Re: [gmx-users] forcefield parameter for bromide ion

[Smith, Micholas D.]

If you are not restricted to the Amber or charmm force-fields for your protein, 
I believe OPLS-AA has Br- anions. Note that ions in traditional 
(non-polarizable) force fields are far from perfect so be careful when 
simulating with them if you concentration is above a few hundred millimolar.

-Micholas

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of jagannath 
mondal 
Sent: Friday, October 09, 2015 3:49 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] forcefield parameter for bromide ion

Hi
  I need to do a simulation of protein in presence of LiBr salt solution.
However, I am not finding any force field parameters for bromide ion either
in charmm forcefields or amber forcefields. Can someone suggest a decent
source for bromide ion forcefield parameters that one could employ in
simulation involving protein.
Jagannath
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Re: [gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)

[Justin Lemkul]

On 10/8/15 11:48 AM, Nicolas Cheron wrote:

Dear all,

I am joining a project where people are using the CHARMM22 force field.
They converted a .prmtop file from Amber to Gromacs format with acpype. In
the output topology, there are no Urey-Bradley potentials or improper
dihedrals (for example, all the [ angle ] functions are of type 1 and none
are 5 and all the [ dihedrals ] function are of type 9 and none are 2).

I am confused, and I am wondering if something went missing when using
acpype? Do you know how acpype handle this part of the amber topology? Or
did acpype converted the Urey-Bradley and improper dihedrals from the
.prmtop to other kind of functions? For an angle A-B-C with Urey-Bradley, I
thought it would be possible to have a force as if there was a bond between
A and C but I didn't find anything like that in the topology.

The manual says about Urey-Bradley potential "Although this can be easily
written as a simple sum of two terms, it is convenient to have it as a
single entry in the topology file and in the output as a separate energy
term" but I am not sure to understand if that means that Gromacs developers
have prefered to keep it as a single entry or not.



Yes, it is a single entry.

Not all U-B angles in CHARMM have an explicit 1-3 term, but if the conversion is 
simply nixing those that exist, clearly the conversion is being done wrong.  If 
impropers are present yet disappearing, this is more evidence that the program 
is not designed to do what you want it to, or that there is some problem with 
the input itself.


The simplest test is to do a single-point energy in AMBER and GROMACS and 
compare the outcome to determine if the newly generated topology is sensible. 
If there's a mismatch, find a better method of conversion.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Virtual sites error

[Erik Marklund]

If memory serves me right, the atom type for the carbon in the thymine ring 
lacks default constraint lengths to the dummy masses. That combination of atom 
types are not used for aminoacids. You will need to calculate what constraint 
lengths yield the correct geometry for the CH3-group, which is quite doable. It 
is sometimes pointed out however, here and elsewhere, that no vsite parameters 
have been rigorously tested for nucleic acids, only for proteins (to my 
knowledge).

Kind regards,
Erik

> On 9 Oct 2015, at 11:55, Timofey Tyugashev  wrote:
> 
> 
> This looks very strange that from the whole assortment of the molecules in 
> the force field only a humble methyl group in thymine lacks proper definition 
> causes such an error.
> Even nucleotides which I added myself to the force field files don't produce 
> any errors
> Is there any way to remedy this without significant hassle? What things are 
> exactly lacking?
>> --
>> 
>> Message: 4
>> Date: Thu, 8 Oct 2015 11:15:17 +
>> From: Erik Marklund 
>> To: "gmx-us...@gromacs.org" 
>> Subject: Re: [gmx-users] Virtual sites error
>> Message-ID: <89ae0bec-6d9f-49a0-83e2-5ad8d7734...@chem.ox.ac.uk>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> Unfortunately, the parameters required for certain virtual sites in nucleic 
>> acids are not define in the force field files that are shipped with Gromacs.
>> 
>> Erik Marklund, PhD
>> Postdoctoral Research Fellow
>> Fulford JRF, Somerville College
>> 
>> Department of Chemistry
>> Physical & Theoretical Chemistry Laboratory
>> University of Oxford
>> South Parks Road
>> Oxford
>> OX1 3QZ
>> 
>>> On 7 Oct 2015, at 11:33, Timofey Tyugashev  wrote:
>>> 
>>> Trying to add hydrogen virtual sites to the model (using -vsites h option 
>>> in pdb2gmx) results in a salvo of error messages when running grommp to 
>>> create .tpr file after the solvation:
>>> 
>>> ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
>>>  No default Constr. No Conn. types
>>> 
>>> 
>>> ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
>>>  No default Constr. No Conn. types
>>> 
>>> This lines in constraints section in the .itp file refer to pairs of two 
>>> MCH3 and one MC atoms, which should serve (the way I understand the 
>>> situation) as replacement methyl group in thymine. There are several more 
>>> pairs of same errors corresponding to different thymine methyl groups in 
>>> the DNA strands.
>>> 
>>> Here is the relevant sections of the itp file for the first two errors:
>>> 
>>> [ constraints ]
>>> ;  aiaj functc0c1
>>>2 3 2
>>>  110   111 2
>>>  110   112 2
>>>  111   112 2
>>> 
>>> [ atoms ]
>>> 
>>>   110 CM321 DT C5110 0.0025 12.01   ; qtot 
>>> -2.867
>>>   111   MCH3321 DT   MC71111  0 7.517   ; qtot 
>>> -2.867
>>>   112   MCH3321 DT   MC72111  0 7.517   ; qtot 
>>> -2.867
>>> -- 
>>> Gromacs Users mailing list
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