[gmx-users] Re: Born-Mayer-Huggins type pair potential

[Dr. Vitaly Chaban]

> Hi!
> I would like to simulate halkali halides in GROMACS by using the Tosi-Fumi
> potential.
>
> The potential is of this kind (Born Mayer Huggins), with an exponential, a
> 6th, 8th powers and the coulomb term:
>
> U(r) = Ae^(-r/rho)  - C/r^6  -D/r^8 + (q1 q2)/(4 pi eps r)
>
> Did somebody used anything of this kind? Is there a way to use this
> potential in GROMACS? Do you have any suggestions?


Tabulate it.


Dr. Vitaly Chaban
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Re: [gmx-users] .top file from .tpr and .xtc

[shahid nayeem]

Hi
To be more clear I have .xtc file for a disulfide linked complex of
two chains. From this trajectory I can extract .xtc file for
individual chains. But when I generate .top file from individual chain
pdb I get one atom extra in .top file i.e. protonated SG of Cys which
I dont need in order to make my .xtc and .top file compatible.
Shahid

On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul  wrote:
>
>
> On 3/18/13 12:35 PM, shahid nayeem wrote:
>>
>> Hi
>> Is it possible to write .top file from .xtc and .tpr using index.ndx
>> so that .top is available for tailormade components of simulated
>> protein.
>>
>
> All topology information is in the .tpr, but not in .top format.  You may be
> able to post-process the output of gmxdump to produce some hacked version,
> but that's just a bit of a hand-waving guess.  I don't really understand
> what your objective is.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] topology

[Justin Lemkul]

On 3/18/13 10:49 PM, shahid nayeem wrote:

I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
shahid



My apologies.  For some reason I always think there is a -cys option, when in 
fact it is -ss.  In any case, if you're trying to treat some strange form of 
cysteine, some force fields have special names for different forms (CYM for 
thiolate, etc) so naming and proper force field choice may be the only viable 
mechanism here.


-Justin


On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul  wrote:



On 3/18/13 10:39 AM, shahid nayeem wrote:


Hi All
   How can I get a topology file using pdb2gmx from a single chain
polypeptide with one of the CYS, SH in the form of SG as if it is
involved in disulfide linkage, while the other chain with which I
expect it to form disulfide link is not in the input pdb file. or can
I use pdb2gmx command and get the separate .top and .gro file for each
chain using index file.



You may be able to use the -cys option to fool pdb2gmx, but I don't know if
that will cause problems.  Having half a disulfide present is odd, though
some force fields support thiolate or neutral (i.e. radical) forms of
cysteine.  You'll have to look into the force field files to see what's
available.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] topology

[shahid nayeem]

I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
shahid

On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul  wrote:
>
>
> On 3/18/13 10:39 AM, shahid nayeem wrote:
>>
>> Hi All
>>   How can I get a topology file using pdb2gmx from a single chain
>> polypeptide with one of the CYS, SH in the form of SG as if it is
>> involved in disulfide linkage, while the other chain with which I
>> expect it to form disulfide link is not in the input pdb file. or can
>> I use pdb2gmx command and get the separate .top and .gro file for each
>> chain using index file.
>>
>
> You may be able to use the -cys option to fool pdb2gmx, but I don't know if
> that will cause problems.  Having half a disulfide present is odd, though
> some force fields support thiolate or neutral (i.e. radical) forms of
> cysteine.  You'll have to look into the force field files to see what's
> available.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Constrain boxsize

[Justin Lemkul]

On 3/18/13 9:59 PM, Kieu Thu Nguyen wrote:

Thank Justin !
I made this rectangular box from merging two cubic boxes. And i carry out
equilibrate this box. Do you mean that i should run NVT, and next step run
NPT, to keep box shape fixed ?



I'm not making any recommendation.  You haven't provided nearly enough 
information to do so.  Are the two liquids miscible?  If they are, then the 
outcome you reported before is to be expected.  If they should not mix, then you 
still have a problem.  You need to post a complete description of what you're 
working with, .mdp file(s) used, and ideally links to screenshots that show the 
behavior you are describing.  Without that information, it's largely guesswork 
as to what's really going on.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Born-Mayer-Huggins type pair potential

[Justin Lemkul]

On 3/18/13 7:49 PM, Gabriele Lanaro wrote:

Hi!
I would like to simulate halkali halides in GROMACS by using the Tosi-Fumi
potential.

The potential is of this kind (Born Mayer Huggins), with an exponential, a
6th, 8th powers and the coulomb term:

U(r) = Ae^(-r/rho)  - C/r^6  -D/r^8 + (q1 q2)/(4 pi eps r)

Did somebody used anything of this kind? Is there a way to use this
potential in GROMACS? Do you have any suggestions?



Tabulated potentials are probably the most painless route.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] Re: polymer duplicate atoms

[Dallas Warren]

As noted by your rtp entry:

>   [ bonds ]
> C1-C4
> C1H11
> C1H12
> C1C2
> C2F21
> C2F22
> C2+C3
> C3F31
> C3F32
> C3C4
> C4F4
> C4Cl4
> C4+C1

One end of the residue bonds via the C1 to a C4 in the next residue, and the 
other end of the residue bonds via the C4 to a C1 in the next residue.

Your beginning and ends to your polymer have to show this, which they currently 
do not.  The rtp entry for both of them do not say anything about how they bond 
to the next residue.  It should be more something like this ...

 [ Fbg ]
   [ bonds ]
 C4+C1
 C4H11
 C4H12
 C4H13

 [ Fen ]

   [ bonds ]
 C1-C4
 C1H11
 C1H12
 C1H13

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of cqgzc
> Sent: Tuesday, 19 March 2013 12:50 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
> 
> I have successfully construct the polymer chain of length 1 using the
> OPLS
> force field. The rtp file as follow:
> 
> ; F2311 - this is an internal residue
> [ Fre ]
>   [ atoms ]
> C1opls_135   -0.5681
> H11   opls_1400.2741
> H12   opls_1400.2731
> C2opls_9620.3732
> F21   opls_965   -0.1652
> F22   opls_965   -0.1592
> C3opls_9620.1823
> F31   opls_965   -0.1333
> F32   opls_965   -0.1443
> C4opls_9630.1424
> F4opls_965   -0.1424
> Cl4   opls_1510.0664
>   [ bonds ]
> C1-C4
> C1H11
> C1H12
> C1C2
> C2F21
> C2F22
> C2+C3
> C3F31
> C3F32
> C3C4
> C4F4
> C4Cl4
> C4+C1
> 
> ; Terminal f2311 residue ("beginning" of chain)
> ; designation arbitrary, C1 is -CH3
> [ Fbg ]
>   [ atoms ]
> C1opls_135   -0.565 1
> H11   opls_1400.198 1
> H12   opls_1400.208 1
> H13   opls_1400.209 1
>   [ bonds ]
> C1H11
> C1H12
> C1H13
> ; Terminal f2311 residue ("end" of chain)
> ; designation arbitrary, C1 is -CH3
> [ Fen ]
>   [ atoms ]
> C1opls_135   -0.7051
> H11   opls_1400.2481
> H12   opls_1400.2461
> H13   opls_1400.2451
>   [ bonds ]
> C1H11
> C1H12
> C1H13
> 
> 
> 
> 
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-
> tp5006328p5006428.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Constrain boxsize

[Kieu Thu Nguyen]

Thank Justin !
I made this rectangular box from merging two cubic boxes. And i carry out
equilibrate this box. Do you mean that i should run NVT, and next step run
NPT, to keep box shape fixed ?

Regards,
~Thu


On Tue, Mar 19, 2013 at 3:39 AM, Justin Lemkul  wrote:

>
>
> On 3/18/13 1:36 PM, Kieu Thu Nguyen wrote:
>
>> Dear All,
>>
>> I want to equilibrate a rectangular box. But after running MD 60 ns, the
>> system become to be a cubic box mostly. I do not want this happens. Can
>> anyone tell me how to constrain the boxsize. In that case, the boxsize has
>> fluctuations but remains the same box-type.
>>
>>
> If the box shape changes drastically, that usually indicates instability
> in the system.  A stable simulation will preserve the original unit cell
> shape.  There is no special way to constrain it to behave as you want it
> to.  NVT keeps the box dimensions fixed, but that doesn't seem to be what
> you want.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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[gmx-users] Re: polymer duplicate atoms

[cqgzc]

I have successfully construct the polymer chain of length 1 using the OPLS
force field. The rtp file as follow:

; F2311 - this is an internal residue
[ Fre ]
  [ atoms ]
C1opls_135   -0.5681
H11   opls_1400.2741
H12   opls_1400.2731
C2opls_9620.3732
F21   opls_965   -0.1652
F22   opls_965   -0.1592
C3opls_9620.1823
F31   opls_965   -0.1333
F32   opls_965   -0.1443
C4opls_9630.1424
F4opls_965   -0.1424
Cl4   opls_1510.0664
  [ bonds ]
C1-C4
C1H11
C1H12
C1C2
C2F21
C2F22
C2+C3
C3F31
C3F32
C3C4
C4F4
C4Cl4
C4+C1

; Terminal f2311 residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
[ Fbg ]
  [ atoms ]
C1opls_135   -0.565 1
H11   opls_1400.198 1
H12   opls_1400.208 1
H13   opls_1400.209 1
  [ bonds ]
C1H11
C1H12
C1H13
; Terminal f2311 residue ("end" of chain)
; designation arbitrary, C1 is -CH3
[ Fen ]
  [ atoms ]
C1opls_135   -0.7051
H11   opls_1400.2481
H12   opls_1400.2461
H13   opls_1400.2451
  [ bonds ]
C1H11
C1H12
C1H13




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[gmx-users] Born-Mayer-Huggins type pair potential

[Gabriele Lanaro]

Hi!
I would like to simulate halkali halides in GROMACS by using the Tosi-Fumi
potential.

The potential is of this kind (Born Mayer Huggins), with an exponential, a
6th, 8th powers and the coulomb term:

U(r) = Ae^(-r/rho)  - C/r^6  -D/r^8 + (q1 q2)/(4 pi eps r)

Did somebody used anything of this kind? Is there a way to use this
potential in GROMACS? Do you have any suggestions?

Thank you,

Gabriele
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Re: [gmx-users] Desired density - genbox

[Justin Lemkul]

On 3/18/13 6:14 PM, Steven Neumann wrote:

On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul  wrote:



On 3/18/13 2:56 PM, Steven Neumann wrote:


Dear Gmx Users,

I am trying to obtain given density for my system for a given molecule
- its a cubic box of 5 nm in dimension.

I calculated that I need 850 molecules to get the density of 500 g/mol
In my box there is already 1 molecule so I try:

genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb



Added 819 molecules (out of 849 requested)
Output configuration contains 9020 atoms in 820 residues
Volume : 125 (nm^3)
Density: 480.336 (g/l)
Number of SOL molecules:  0

How can I add 30 more molecules using gromacs? I want to avoid adding
it manually.



Use a larger box and equilibrate.


Thanks.
Larger box will need more molecules which is quite obvious so the same
problem occurs. I need a cubic box first with given fixed density and
then equilibrate it. Further step is to extend the box in one
dimension to get properties I want.
Shall manually add them then?



I think you missed the point of what I was saying.  You can use a larger box, 
with 850 molecules inserted, and equilbrate under NPT (using isotropic pressure 
coupling to guarantee the box stays cubic).  Provided the force field model 
produces the density you want, that's all you need to do.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Desired density - genbox

[Steven Neumann]

On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul  wrote:
>
>
> On 3/18/13 2:56 PM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I am trying to obtain given density for my system for a given molecule
>> - its a cubic box of 5 nm in dimension.
>>
>> I calculated that I need 850 molecules to get the density of 500 g/mol
>> In my box there is already 1 molecule so I try:
>>
>> genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb
>>
>>
>>
>> Added 819 molecules (out of 849 requested)
>> Output configuration contains 9020 atoms in 820 residues
>> Volume : 125 (nm^3)
>> Density: 480.336 (g/l)
>> Number of SOL molecules:  0
>>
>> How can I add 30 more molecules using gromacs? I want to avoid adding
>> it manually.
>>
>
> Use a larger box and equilibrate.

Thanks.
Larger box will need more molecules which is quite obvious so the same
problem occurs. I need a cubic box first with given fixed density and
then equilibrate it. Further step is to extend the box in one
dimension to get properties I want.
Shall manually add them then?


Steven
 All genbox tries to do is add molecules
> randomly, which is not a foolproof process.  If the force field parameters
> indeed produce the correct density, you should be able to produce it rather
> quickly.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Desired density - genbox

[Justin Lemkul]

On 3/18/13 2:56 PM, Steven Neumann wrote:

Dear Gmx Users,

I am trying to obtain given density for my system for a given molecule
- its a cubic box of 5 nm in dimension.

I calculated that I need 850 molecules to get the density of 500 g/mol
In my box there is already 1 molecule so I try:

genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb



Added 819 molecules (out of 849 requested)
Output configuration contains 9020 atoms in 820 residues
Volume : 125 (nm^3)
Density: 480.336 (g/l)
Number of SOL molecules:  0

How can I add 30 more molecules using gromacs? I want to avoid adding
it manually.



Use a larger box and equilibrate.  All genbox tries to do is add molecules 
randomly, which is not a foolproof process.  If the force field parameters 
indeed produce the correct density, you should be able to produce it rather quickly.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Constrain boxsize

[Justin Lemkul]

On 3/18/13 1:36 PM, Kieu Thu Nguyen wrote:

Dear All,

I want to equilibrate a rectangular box. But after running MD 60 ns, the
system become to be a cubic box mostly. I do not want this happens. Can
anyone tell me how to constrain the boxsize. In that case, the boxsize has
fluctuations but remains the same box-type.



If the box shape changes drastically, that usually indicates instability in the 
system.  A stable simulation will preserve the original unit cell shape.  There 
is no special way to constrain it to behave as you want it to.  NVT keeps the 
box dimensions fixed, but that doesn't seem to be what you want.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Problem in adding *.itp for 2 different ligands in topol .top

[Justin Lemkul]

On 3/18/13 12:47 PM, Parshvika Sharma wrote:

Dear gromacs users,

I want to run a protein ligand MD in Gromacs 4.6 using CHARMM forcefield.
My system consists of 2 non-covalently bound ligands (FAD and NADPH) in the
active site. I generated the topology files (*.itp) of ligands using
SWISSPARAM. Before running the energy minimization, I added the *.itp file
for both ligands in topol.top file as mentioned in the gromacs tutorial.

#include "charmm27.ff/forcefield.itp"
#include "FAD.itp"
#include "NDP.itp"

But while running GROMPP I am getting this error,

Syntax error - File NDP.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

It just accepts the first *.itp mentioned in the topol.top, be it FAD.itp
or NDP.itp and shows this error for the file mentioned next.

I would like to know the correct way to mention *.itp  in topol.top, if we
have more than 1 ligand.



If each .itp file introduces new [atomtypes], you can't simply #include them. 
All [atomtypes] (like any force field-level directive) must be declared before 
any [moleculetype] is declared.  I posted a detailed explanation of this within 
the last few weeks (hint: check the archive, most topics like this have been 
discussed at length many times).


Net effect?  Merge the two [atomtypes] directives before #including any new 
[moleculetype] blocks.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] .top file from .tpr and .xtc

[Justin Lemkul]

On 3/18/13 12:35 PM, shahid nayeem wrote:

Hi
Is it possible to write .top file from .xtc and .tpr using index.ndx
so that .top is available for tailormade components of simulated
protein.



All topology information is in the .tpr, but not in .top format.  You may be 
able to post-process the output of gmxdump to produce some hacked version, but 
that's just a bit of a hand-waving guess.  I don't really understand what your 
objective is.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
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jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] topology

[Justin Lemkul]

On 3/18/13 10:39 AM, shahid nayeem wrote:

Hi All
  How can I get a topology file using pdb2gmx from a single chain
polypeptide with one of the CYS, SH in the form of SG as if it is
involved in disulfide linkage, while the other chain with which I
expect it to form disulfide link is not in the input pdb file. or can
I use pdb2gmx command and get the separate .top and .gro file for each
chain using index file.



You may be able to use the -cys option to fool pdb2gmx, but I don't know if that 
will cause problems.  Having half a disulfide present is odd, though some force 
fields support thiolate or neutral (i.e. radical) forms of cysteine.  You'll 
have to look into the force field files to see what's available.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Problem in adding *.itp for 2 different ligands in topol .top

[Parshvika Sharma]

Dear gromacs users,

I want to run a protein ligand MD in Gromacs 4.6 using CHARMM forcefield.
My system consists of 2 non-covalently bound ligands (FAD and NADPH) in the
active site. I generated the topology files (*.itp) of ligands using
SWISSPARAM. Before running the energy minimization, I added the *.itp file
for both ligands in topol.top file as mentioned in the gromacs tutorial.

#include "charmm27.ff/forcefield.itp"
#include "FAD.itp"
#include "NDP.itp"

But while running GROMPP I am getting this error,

Syntax error - File NDP.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

It just accepts the first *.itp mentioned in the topol.top, be it FAD.itp
or NDP.itp and shows this error for the file mentioned next.

I would like to know the correct way to mention *.itp  in topol.top, if we
have more than 1 ligand.


Thank you
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Re: [gmx-users] pull code - constraint pulling - forces are zeros

[Erik Marklund]

Hi,

I believe there is no force output for constraint pulling. Try umbrella.

Erik

On Mar 18, 2013, at 3:28 PM, raghav singh wrote:


Hello Fellow Users,

I am trying to pull a DNA molecule. I have fixed one end and trying  
to pull

the other one using this .mdp file.. force output is all zeros.
I have tried going through the user-list but have not found any  
solution

yet. I am using gmx-version 4.5.5.

Any idea why is it happening.??
below is the mdp file i am using.

Thank you
Raghav

##

title   = constraint pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 2; 1ns
nstcomm = 10
; Output parameters
nstxout = 100  ; every 10 ps
nstvout = 100
nstfout = 20
nstxtcout   = 20  ; every 1 ps
nstenergy   = 20
energygrps  = DNA Water_and_ions
; Bond parameters
constraint_algorithm= lincs
lincs_iter  = 1
lincs_order = 4
constraints = all-bonds
continuation= no   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.2
rcoulomb= 1.2
rvdw= 1.2
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = V-rescale
tc_grps = DNA   Water_and_ions
tau_t   = 0.1   0.1
ref_t   = 310   310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 2.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = yes
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= constraint
pull_geometry   = distance  ; simple distance increase
pull_dim= N Y N
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Fixed
pull_group1 = Pull
pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 500

###
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[gmx-users] topology

[shahid nayeem]

Hi All
 How can I get a topology file using pdb2gmx from a single chain
polypeptide with one of the CYS, SH in the form of SG as if it is
involved in disulfide linkage, while the other chain with which I
expect it to form disulfide link is not in the input pdb file. or can
I use pdb2gmx command and get the separate .top and .gro file for each
chain using index file.

shahid
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[gmx-users] pull code - constraint pulling - forces are zeros

[raghav singh]

Hello Fellow Users,

I am trying to pull a DNA molecule. I have fixed one end and trying to pull
the other one using this .mdp file.. force output is all zeros.
I have tried going through the user-list but have not found any solution
yet. I am using gmx-version 4.5.5.

Any idea why is it happening.??
below is the mdp file i am using.

Thank you
Raghav

##

title   = constraint pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 2; 1ns
nstcomm = 10
; Output parameters
nstxout = 100  ; every 10 ps
nstvout = 100
nstfout = 20
nstxtcout   = 20  ; every 1 ps
nstenergy   = 20
energygrps  = DNA Water_and_ions
; Bond parameters
constraint_algorithm= lincs
lincs_iter  = 1
lincs_order = 4
constraints = all-bonds
continuation= no   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.2
rcoulomb= 1.2
rvdw= 1.2
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = V-rescale
tc_grps = DNA   Water_and_ions
tau_t   = 0.1   0.1
ref_t   = 310   310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 2.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = yes
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= constraint
pull_geometry   = distance  ; simple distance increase
pull_dim= N Y N
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Fixed
pull_group1 = Pull
pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 500

###
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Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X

[Per Larsson]

Thanks  - I have filed issue #1194 and assigned it to David.
http://redmine.gromacs.org/issues/1194

Let me know if there is anything else that is needed. I could take a shot at 
myself, and will play around with it, but I don't know the details of the 
symtab in any detail, unfortunately. 

15 mar 2013 kl. 19:51 skrev David van der Spoel:
>> 
>> Taking away the restraint allows me to start the run in 4.6.1, and also 
>> reformatting the [ dihedral_restraint ] section to comply with 4.6 works.
>> Is this a know issue, am I missing something obvious, or should I file an 
>> issue on redmine?
> 
> redmine please.
> 
>> 
>> Thanks
>> /Per--
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> 
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: Fw: Fwd: [gmx-users] position restraints

[Justin Lemkul]

On Mon, Mar 18, 2013 at 8:24 AM, Shima Arasteh
wrote:

> Yes, I overcome the last problems and I could see the pos.rest energy term
> in my log file.
> In order to create the itp files to include in top file, I opened the gro
> file which I entered as an input in my mdrun command. How might I check
> this issue that all the atoms in itp groups are  involved in position
> restraints? Is there any solutions to check it?
>
>
The input coordinate file doesn't tell you anything. Load the trajectory
and watch it. If atoms are moving that shouldn't be, you have a problem.
Inspect the position restraint .itp file to see which atoms it covers, and
cross-reference those with the chain topologies to make sure the atoms you
think are being restrained actually are.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: Fw: Fwd: [gmx-users] position restraints

[Shima Arasteh]

Yes, I overcome the last problems and I could see the pos.rest energy term in 
my log file.
In order to create the itp files to include in top file, I opened the gro file 
which I entered as an input in my mdrun command. How might I check this issue 
that all the atoms in itp groups are  involved in position restraints? Is there 
any solutions to check it?

Many many thanks for your replies

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Monday, March 18, 2013 4:46 PM
Subject: Re: Fw: Fwd: [gmx-users] position restraints



On 3/18/13 6:02 AM, Shima Arasteh wrote:
> With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I 
> don't know if this range of deviation with position restraints is sensible or 
> not! I can't believe with such a force of 10 I still see deviations!
>
> I'd prefer to get less deviation. Would it be possible by using a greater fc 
> ? Is it sensible?
>

Were restraints correctly applied?  Your last messages indicated fatal errors 
in 
trying to apply restraints - have you overcome those problems?  Is there a 
position restraint energy term written to the .log and .edr files?  Using such 
a 
huge force constant should not result in such RMSD values unless (1) they are 
not being applied or (2) whatever groups you have created for applying 
restraints do not cover all atoms that are being analyzed in the RMSD 
calculation, i.e. some are unrestrained and moving normally when you think they 
are being restrained.

-Justin

>
> Thanks for your suggestions in advance.
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc:
> Sent: Saturday, March 16, 2013 12:24 AM
> Subject: Re: Fw: Fwd: [gmx-users] position restraints
>
>
>
> On 3/15/13 8:50 AM, Shima Arasteh wrote:
>> Dear users,
>>
>>
>> Although I put the position restraints on backbone, I get RMSD around 0.2 
>> nm. Is it usual?
>
> No, 0.2 nm is very high.  With position restraints, offhand I would think 
> around
> 0.05 nm or less would be indicative of proper restraints.
>
>> This deviation is just for a minimization step only. I' m on doubt about 
>> keeping the backbone in a fix secondary structure.
>> I' d prefer to restraint the backbone completely. Is it possible?
>>
>
> Yes, using genrestr to create a suitable posre.itp file that includes only
> backbone atoms.
>
> -Justin
>
>> Thanks in advance.
>>
>>
>>
>> Restraints allow, by definition, for slight deviations.
>>
>> Erik
>> * Please don't post (un)subscribe requests to the list. Use thewww interface 
>> or send it to gmx-users-requ...@gromacs.org.
>>
>>
>>
>>
>> Dear gmx users,
>>
>> I want to use restraints on backbone of my protein to keep its secondary
>>     structure during minimization and equilibration steps. To do so, I
>> generated backbone-restrain.itp and then included it to top file. Next,
>> added define = -DPOSRES to minim.mdp file.
>> After minimization, when I check the minimization output file, I saw
>> that the backbone of input and output files are not exactly the same.
>> Is there any step which I have not done to set the restraints correctly?
>>
>>
>> Thanks in advance.
>>
>> Sincerely,
>> Shima
>>
>

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: Fwd: Fw: Fwd: [gmx-users] position restraints

[Mark Abraham]

On Mon, Mar 18, 2013 at 1:15 PM, Justin Lemkul  wrote:

>
>
> On 3/18/13 3:42 AM, Shima Arasteh wrote:
>
>> Thanks for all your replies.
>> But I' d like to know what the meanings of S and D are? Why sometimes we
>> should write DPOSRE, sometimes POSRE, and sometimes DPOSRES?
>>
>>
> I already explained what the "D" prefix means.  If this is unclear to you,
> please read about cpp macros.  When processing a topology, grompp works
> just like cpp works on C source code.
>

See also http://www.gromacs.org/Documentation/Include_File_Mechanism

Mark

The choice between POSRE and POSRES is completely irrelevant except for
> your own usage and consistency in so doing.  Gromacs defaults to using
> POSRES to indicate POSition REStraints.  If you build some custom topology,
> you can use whatever you want.  it doesn't matter at all, as long as you
> are consistent in invoking it.
>
> -Justin
>
>
>
>>
>> Sincerely,
>> Shima
>>
>>
>> __**__
>> From: Shima Arasteh 
>> To: Justin Lemkul ; Discussion list for GROMACS users <
>> gmx-users@gromacs.org>
>> Sent: Monday, March 18, 2013 10:35 AM
>> Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
>>
>> To solve the problem, I changed all DPOSREs in if statments to POSRE.
>> Again I get the fatal error. This error states that I have inserted
>> topology section "position_restraints" in a wrong place. I checked again
>> the itp files included in my top file. They are matched correctly!  Did I
>> modified the settings incorrectly?
>>
>> What would be other potent problems?
>>
>> Please help me.
>> Thanks for your help.
>>
>>
>>
>> Sincerely,
>> Shima
>>
>>
>> - Original Message -
>> From: Justin Lemkul 
>> To: Shima Arasteh ; Discussion list for
>> GROMACS users 
>> Cc:
>> Sent: Sunday, March 17, 2013 5:19 PM
>> Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
>>
>>
>>
>> On 3/17/13 6:50 AM, Shima Arasteh wrote:
>>
>>> Thanks for your replies.
>>> As you suggested, I did as follows:
>>> 1. made index groups of two chains of my protein
>>> 2.Then applied genrestr in this command to generate 2 itp files:
>>> chainA_posre.itp and chainB_posre.itp
>>> #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10
>>> 10 -n index-chain.ndx
>>> #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10
>>> 10 -n index-chain.ndx
>>>
>>> 3.Next, I included the itp files as follow in my top file:
>>>
>>> ; Include chain topologies
>>> #include "topol_Protein_chain_A.itp"
>>> #ifdef DPOSRE
>>> #include "chainA_posre.itp"
>>> #endif
>>> #include "topol_Protein_chain_B.itp"
>>> #ifdef DPOSRE
>>> #include "chainB_posre.itp"
>>> #endif
>>>
>>> 4. I also added this line to my mdp file:
>>> define = -DPOSRE
>>>
>>> 5. In addition I added these at the top of itp files for bothe
>>> restrained chains:
>>> #ifdef DPOSRE
>>> #endif
>>>
>>> Now when I run the command :
>>> grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr
>>>
>>> I don't get any errors.
>>> But when I run the mdrun I don't see any position restraint terms in my
>>> log file.
>>> Would you please let me know your suggestions in this about? Did I do
>>> any steps by mistake?
>>>
>>>
>> Yes, again there is a problem with the #ifdef statements.  If you use:
>>
>> #ifdef DPOSRE
>> ...
>> #endif
>>
>> the corresponding "define" statement is -DDPOSRE.  Think of the first "D"
>> in the
>> "define" statement as "I am defining the following string to be true."
>>  Your
>> .mdp file corresponds to the use of:
>>
>> #ifdef POSRE
>> ...
>> #endif
>>
>> -Justin
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
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Re: Fw: Fwd: [gmx-users] position restraints

[Justin Lemkul]

On 3/18/13 6:02 AM, Shima Arasteh wrote:

With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I 
don't know if this range of deviation with position restraints is sensible or 
not! I can't believe with such a force of 10 I still see deviations!

I'd prefer to get less deviation. Would it be possible by using a greater fc ? 
Is it sensible?



Were restraints correctly applied?  Your last messages indicated fatal errors in 
trying to apply restraints - have you overcome those problems?  Is there a 
position restraint energy term written to the .log and .edr files?  Using such a 
huge force constant should not result in such RMSD values unless (1) they are 
not being applied or (2) whatever groups you have created for applying 
restraints do not cover all atoms that are being analyzed in the RMSD 
calculation, i.e. some are unrestrained and moving normally when you think they 
are being restrained.


-Justin



Thanks for your suggestions in advance.


Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Cc:
Sent: Saturday, March 16, 2013 12:24 AM
Subject: Re: Fw: Fwd: [gmx-users] position restraints



On 3/15/13 8:50 AM, Shima Arasteh wrote:

Dear users,


Although I put the position restraints on backbone, I get RMSD around 0.2 nm. 
Is it usual?


No, 0.2 nm is very high.  With position restraints, offhand I would think around
0.05 nm or less would be indicative of proper restraints.


This deviation is just for a minimization step only. I' m on doubt about 
keeping the backbone in a fix secondary structure.
I' d prefer to restraint the backbone completely. Is it possible?



Yes, using genrestr to create a suitable posre.itp file that includes only
backbone atoms.

-Justin


Thanks in advance.



Restraints allow, by definition, for slight deviations.

Erik
* Please don't post (un)subscribe requests to the list. Use thewww interface or 
send it to gmx-users-requ...@gromacs.org.




Dear gmx users,

I want to use restraints on backbone of my protein to keep its secondary
structure during minimization and equilibration steps. To do so, I
generated backbone-restrain.itp and then included it to top file. Next,
added define = -DPOSRES to minim.mdp file.
After minimization, when I check the minimization output file, I saw
that the backbone of input and output files are not exactly the same.
Is there any step which I have not done to set the restraints correctly?


Thanks in advance.

Sincerely,
Shima





--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: Fwd: Fw: Fwd: [gmx-users] position restraints

[Justin Lemkul]

On 3/18/13 3:42 AM, Shima Arasteh wrote:

Thanks for all your replies.
But I' d like to know what the meanings of S and D are? Why sometimes we should 
write DPOSRE, sometimes POSRE, and sometimes DPOSRES?



I already explained what the "D" prefix means.  If this is unclear to you, 
please read about cpp macros.  When processing a topology, grompp works just 
like cpp works on C source code.


The choice between POSRE and POSRES is completely irrelevant except for your own 
usage and consistency in so doing.  Gromacs defaults to using POSRES to indicate 
POSition REStraints.  If you build some custom topology, you can use whatever 
you want.  it doesn't matter at all, as long as you are consistent in invoking it.


-Justin




Sincerely,
Shima



From: Shima Arasteh 
To: Justin Lemkul ; Discussion list for GROMACS users 

Sent: Monday, March 18, 2013 10:35 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints

To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the 
fatal error. This error states that I have inserted topology section 
"position_restraints" in a wrong place. I checked again the itp files included 
in my top file. They are matched correctly!  Did I modified the settings incorrectly?

What would be other potent problems?

Please help me.
Thanks for your help.



Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Cc:
Sent: Sunday, March 17, 2013 5:19 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints



On 3/17/13 6:50 AM, Shima Arasteh wrote:

Thanks for your replies.
As you suggested, I did as follows:
1. made index groups of two chains of my protein
2.Then applied genrestr in this command to generate 2 itp files: 
chainA_posre.itp and chainB_posre.itp
#genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 
-n index-chain.ndx
#genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 
-n index-chain.ndx

3.Next, I included the itp files as follow in my top file:

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef DPOSRE
#include "chainA_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef DPOSRE
#include "chainB_posre.itp"
#endif

4. I also added this line to my mdp file:
define = -DPOSRE

5. In addition I added these at the top of itp files for bothe restrained 
chains:
#ifdef DPOSRE
#endif

Now when I run the command :
grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr

I don't get any errors.
But when I run the mdrun I don't see any position restraint terms in my log 
file.
Would you please let me know your suggestions in this about? Did I do any steps 
by mistake?



Yes, again there is a problem with the #ifdef statements.  If you use:

#ifdef DPOSRE
...
#endif

the corresponding "define" statement is -DDPOSRE.  Think of the first "D" in the
"define" statement as "I am defining the following string to be true."  Your
.mdp file corresponds to the use of:

#ifdef POSRE
...
#endif

-Justin



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: Fwd: Fw: Fwd: [gmx-users] position restraints

[Justin Lemkul]

On 3/18/13 3:05 AM, Shima Arasteh wrote:

To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the 
fatal error. This error states that I have inserted topology section 
"position_restraints" in a wrong place. I checked again the itp files included 
in my top file. They are matched correctly!  Did I modified the settings incorrectly?



Clearly.  Fatal errors mean something is very wrong.  In principle, what you 
showed before was correct.  If that wasn't an actual topology snippet or you've 
done something else wrong, then I haven't seen what it is.


-Justin


What would be other potent problems?

Please help me.
Thanks for your help.



Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Cc:
Sent: Sunday, March 17, 2013 5:19 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints



On 3/17/13 6:50 AM, Shima Arasteh wrote:

Thanks for your replies.
As you suggested, I did as follows:
1. made index groups of two chains of my protein
2.Then applied genrestr in this command to generate 2 itp files: 
chainA_posre.itp and chainB_posre.itp
#genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 
-n index-chain.ndx
#genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 
-n index-chain.ndx

3.Next, I included the itp files as follow in my top file:

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef DPOSRE
#include "chainA_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef DPOSRE
#include "chainB_posre.itp"
#endif

4. I also added this line to my mdp file:
define = -DPOSRE

5. In addition I added these at the top of itp files for bothe restrained 
chains:
#ifdef DPOSRE
#endif

Now when I run the command :
grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr

I don't get any errors.
But when I run the mdrun I don't see any position restraint terms in my log 
file.
Would you please let me know your suggestions in this about? Did I do any steps 
by mistake?



Yes, again there is a problem with the #ifdef statements.  If you use:

#ifdef DPOSRE
...
#endif

the corresponding "define" statement is -DDPOSRE.  Think of the first "D" in the
"define" statement as "I am defining the following string to be true."  Your
.mdp file corresponds to the use of:

#ifdef POSRE
...
#endif

-Justin



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] [Fwd: implicit solvation]

[Justin Lemkul]

On 3/18/13 1:36 AM, preetichoudh...@iisermohali.ac.in wrote:




 Original Message 
Subject: implicit solvation
From:preetichoudh...@iisermohali.ac.in
Date:Fri, March 15, 2013 1:58 pm
To:  gmx-users@gromacs.org
--

hi,
I am trying to simulate a 50 residue protein in implicit water.Can anyone
tell me that why we usually set the cuttoff to be 0.
coulombtype = Cut-off
vdwtype = Cut-off
nstype = grid
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0.
I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain
why this is being done.


The choice of whether or not to use constraints comes down to whether you 
believe that a rigid bond or a harmonic one is more appropriate.  What's more, 
constraints allow for larger time steps, and thus more efficient simulations.



Also we dont need to do nvt and npt equlibration here.We dont neutralise
our system too.But it keeps on showing in note:


Notes are just informative messages.  They don't necessarily signal that 
anything is wrong (though they can, in some cases).



NOTE 1 [file topol.top, line 7412]:
   System has non-zero total charge: -2.00
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.

Correct me if I am wrong.
Also while doing production run,I am getting this error:-
WARNING 1 [file topol.top, line 7412]:
   The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG
   has an estimated oscillational period of 9.0e-03 ps, which is less than 5
   times the time step of 2.0e-03 ps.
   Maybe you forgot to change the constraints mdp option.



Your time step is too large in the absence of constraints.  For stability and 
energy conservation, you probably have to use a time step of 1 fs or less, 
probably 0.5 fs.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: Fw: Fwd: [gmx-users] position restraints

[Shima Arasteh]

With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I 
don't know if this range of deviation with position restraints is sensible or 
not! I can't believe with such a force of 10 I still see deviations!

I'd prefer to get less deviation. Would it be possible by using a greater fc ? 
Is it sensible?


Thanks for your suggestions in advance.

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Saturday, March 16, 2013 12:24 AM
Subject: Re: Fw: Fwd: [gmx-users] position restraints



On 3/15/13 8:50 AM, Shima Arasteh wrote:
> Dear users,
>
>
> Although I put the position restraints on backbone, I get RMSD around 0.2 nm. 
> Is it usual?

No, 0.2 nm is very high.  With position restraints, offhand I would think 
around 
0.05 nm or less would be indicative of proper restraints.

> This deviation is just for a minimization step only. I' m on doubt about 
> keeping the backbone in a fix secondary structure.
> I' d prefer to restraint the backbone completely. Is it possible?
>

Yes, using genrestr to create a suitable posre.itp file that includes only 
backbone atoms.

-Justin

> Thanks in advance.
>
>
>
> Restraints allow, by definition, for slight deviations.
>
> Erik
> * Please don't post (un)subscribe requests to the list. Use thewww interface 
> or send it to gmx-users-requ...@gromacs.org.
>
>
>
>
> Dear gmx users,
>
> I want to use restraints on backbone of my protein to keep its secondary
>   structure during minimization and equilibration steps. To do so, I
> generated backbone-restrain.itp and then included it to top file. Next,
> added define = -DPOSRES to minim.mdp file.
> After minimization, when I check the minimization output file, I saw
> that the backbone of input and output files are not exactly the same.
> Is there any step which I have not done to set the restraints correctly?
>
>
> Thanks in advance.
>
> Sincerely,
> Shima
>

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



--
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Re: Fwd: Fw: Fwd: [gmx-users] position restraints

[Shima Arasteh]

Thanks for all your replies.
But I' d like to know what the meanings of S and D are? Why sometimes we should 
write DPOSRE, sometimes POSRE, and sometimes DPOSRES?



Sincerely,
Shima



From: Shima Arasteh 
To: Justin Lemkul ; Discussion list for GROMACS users 
 
Sent: Monday, March 18, 2013 10:35 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints

To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I 
get the fatal error. This error states that I have inserted topology section 
"position_restraints" in a wrong place. I checked again the itp files included 
in my top file. They are matched correctly!  Did I modified the settings 
incorrectly? 

What would be other potent problems?

Please help me.
Thanks for your help.



Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Sunday, March 17, 2013 5:19 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints



On 3/17/13 6:50 AM, Shima Arasteh wrote:
> Thanks for your replies.
> As you suggested, I did as follows:
> 1. made index groups of two chains of my protein
> 2.Then applied genrestr in this command to generate 2 itp files: 
> chainA_posre.itp and chainB_posre.itp
> #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 
> 10 -n index-chain.ndx
> #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 
> 10 -n index-chain.ndx
>
> 3.Next, I included the itp files as follow in my top file:
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #ifdef DPOSRE
> #include "chainA_posre.itp"
> #endif
> #include "topol_Protein_chain_B.itp"
> #ifdef DPOSRE
> #include "chainB_posre.itp"
> #endif
>
> 4. I also added this line to my mdp file:
> define         = -DPOSRE
>
> 5. In addition I added these at the top of itp files for bothe restrained 
> chains:
> #ifdef DPOSRE
> #endif
>
> Now when I run the command :
> grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr
>
> I don't get any errors.
> But when I run the mdrun I don't see any position restraint terms in my log 
> file.
> Would you please let me know your suggestions in this about? Did I do any 
> steps by mistake?
>

Yes, again there is a problem with the #ifdef statements.  If you use:

#ifdef DPOSRE
...
#endif

the corresponding "define" statement is -DDPOSRE.  Think of the first "D" in 
the 
"define" statement as "I am defining the following string to be true."  Your 
.mdp file corresponds to the use of:

#ifdef POSRE
...
#endif

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: Fwd: Fw: Fwd: [gmx-users] position restraints

[Shima Arasteh]

To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I 
get the fatal error. This error states that I have inserted topology section 
"position_restraints" in a wrong place. I checked again the itp files included 
in my top file. They are matched correctly!  Did I modified the settings 
incorrectly? 

What would be other potent problems?

Please help me.
Thanks for your help.

 

Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Sunday, March 17, 2013 5:19 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints



On 3/17/13 6:50 AM, Shima Arasteh wrote:
> Thanks for your replies.
> As you suggested, I did as follows:
> 1. made index groups of two chains of my protein
> 2.Then applied genrestr in this command to generate 2 itp files: 
> chainA_posre.itp and chainB_posre.itp
> #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 
> 10 -n index-chain.ndx
> #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 
> 10 -n index-chain.ndx
>
> 3.Next, I included the itp files as follow in my top file:
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #ifdef DPOSRE
> #include "chainA_posre.itp"
> #endif
> #include "topol_Protein_chain_B.itp"
> #ifdef DPOSRE
> #include "chainB_posre.itp"
> #endif
>
> 4. I also added this line to my mdp file:
> define         = -DPOSRE
>
> 5. In addition I added these at the top of itp files for bothe restrained 
> chains:
> #ifdef DPOSRE
> #endif
>
> Now when I run the command :
> grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr
>
> I don't get any errors.
> But when I run the mdrun I don't see any position restraint terms in my log 
> file.
> Would you please let me know your suggestions in this about? Did I do any 
> steps by mistake?
>

Yes, again there is a problem with the #ifdef statements.  If you use:

#ifdef DPOSRE
...
#endif

the corresponding "define" statement is -DDPOSRE.  Think of the first "D" in 
the 
"define" statement as "I am defining the following string to be true."  Your 
.mdp file corresponds to the use of:

#ifdef POSRE
...
#endif

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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