Re: [gmx-users] Non integer charge value

[Justin Lemkul]

On 5/10/18 8:57 AM, Hemalatha Jayabal wrote:

The magnitude of the charge is 0.18 and I hope such magnitude cannot be
ignored. Please find the topology of the protein chain(specific residue) in
which the error is occuring
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
; residue 202 HYP rtp HYP  q +0.2
  1NH2202HYP  N  1  -0.96 14.007   ;
qtot -0.96
  2  H202HYPHT1  2   0.34  1.008   ;
qtot -0.62
  3  H202HYPHT2  3   0.34  1.008   ;
qtot -0.28


What patching are you applying to the N-terminus? These charges are 
totally wrong. Make sure to apply the PRO-NH2+ patch.


-Justin


  4CT1202HYP CA  4   0.19 12.011   ;
qtot -0.09
  5 HB202HYP HA  5   0.09  1.008   ;
qtot 0
  6  C202HYP  C  6   0.51 12.011   ;
qtot 0.51
  7  O202HYP  O  7  -0.51 15.999   ;
qtot 0
  8CP2202HYP CB  8  -0.18 12.011   ;
qtot -0.18
  9 HA202HYPHB1  9   0.09  1.008   ;
qtot -0.09
 10 HA202HYPHB2 10   0.09  1.008   ;
qtot 0
 11CP2202HYP CG 11   0.14 12.011   ;
qtot 0.14
 12 HA202HYP HG 12   0.09  1.008   ;
qtot 0.23
 13CP3202HYP CD 13  0 12.011   ;
qtot 0.23
 14 HA202HYP   HD21 14   0.09  1.008   ;
qtot 0.32
 15 HA202HYP   HD22 15   0.09  1.008   ;
qtot 0.41
 16OH1202HYPOD1 16  -0.66 15.999   ;
qtot -0.25
 17  H202HYPHD1 17   0.43  1.008   ;
qtot 0.18



On Thu 10 May, 2018, 18:07 Justin Lemkul,  wrote:



On 5/10/18 8:29 AM, Hemalatha Jayabal wrote:

Hi all,

I have added a non standard amino acid 'Hydroxyproline' to my forcefield
(from literature) Charmm27 and after using pdb2gmx i could see that the
system has a non integer charge value for 1 protein chain out of 3

protein

chains.  (All 3 chains contain the non standard amino acid)
   The problem is occuring in the chain in which the terminal residue is

this

hydroxyproline. (All other places where the 'HYP' residue appears, the
charge is 0). I tried using different terminii just to be sure that the
problem is not because of the terminii.

What should be done in such a case?

That depends on if the magnitude of the charge is meaningful or not. If
you have two "correct" chains and one "incorrect" chain, that suggests
that nothing is likely wrong with your HYP residue so things should be
fine, but refer to
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic to be
sure. The current version of GROMACS (2018.1) handles these rounding
issues better to trigger fewer false warnings.

-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.thelemkullab.com

==

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--
==

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.thelemkullab.com

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[gmx-users] calculating work done in SMD using gromacs 5.1.2

[Chinmai P]

Hi all,
I have performed steered MD simulations for pulling ligand through the
tunnel of protein. This is done in three parts where in the first part
ligand is pulled towards the centre of tunnel using COM of residues in the
centre as reference, in second part the ligand is pulled further from
centre to the tip of tunnel by using COM of residues at tip.In the third
part, in order to bring the ligand completely out from protein, it was
pushed out from tip to the exterior of protein Since. the entire trajectory
is divided into 3 parts with different references, I am confused how to
calculate the total work done for pulling ligand from one end of tunnel to
other.
Kindly help.
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[gmx-users] V2018.1 building issues

[kevin chen]

Hi  Gromacs Users,

I'm having this weird issue while trying to build the new V2018.1 on
Stampede2, which has both SKX amd KNL nodes on it. For V2016 and older, in
order to run the same executable(mdrun_mpi), we have to build the "fat"
binary with " -DGMX_SIMD=AVX_512" and "-DCMAKE_C_FLAGS="-O3 -xCORE-AVX2
-axCORE-AVX512,MIC-AVX512 ". That actually worked just fine for V2016. We
can actually run simulation on both skx and knl without any issues using
the same binary. However, for some reason the same trick no longer works
with V2018.1. We tried to build V2018.1 with the exactly same building
script with " -DGMX_SIMD=AVX_512" option applied. This time around the
binary(mdrun_mpi) only works on skx node but no on knls. So I was wondering
is there any thing change since V2016 causing this issue or am I missing
anything here? Thanks advanced for any pointers you guys might provide.

Our building environment,

Currently Loaded Modules:
  1) intel/17.0.4   3) git/2.9.0   5) python/2.7.13   7) TACC
  2) impi/17.0.34) autotools/1.1   6) xalt/1.7.7  8) cmake/3.10.2

Best,

Kevin
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Re: [gmx-users] Non integer charge value

[Hemalatha Jayabal]

The magnitude of the charge is 0.18 and I hope such magnitude cannot be
ignored. Please find the topology of the protein chain(specific residue) in
which the error is occuring
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
  chargeB  massB
; residue 202 HYP rtp HYP  q +0.2
 1NH2202HYP  N  1  -0.96 14.007   ;
qtot -0.96
 2  H202HYPHT1  2   0.34  1.008   ;
qtot -0.62
 3  H202HYPHT2  3   0.34  1.008   ;
qtot -0.28
 4CT1202HYP CA  4   0.19 12.011   ;
qtot -0.09
 5 HB202HYP HA  5   0.09  1.008   ;
qtot 0
 6  C202HYP  C  6   0.51 12.011   ;
qtot 0.51
 7  O202HYP  O  7  -0.51 15.999   ;
qtot 0
 8CP2202HYP CB  8  -0.18 12.011   ;
qtot -0.18
 9 HA202HYPHB1  9   0.09  1.008   ;
qtot -0.09
10 HA202HYPHB2 10   0.09  1.008   ;
qtot 0
11CP2202HYP CG 11   0.14 12.011   ;
qtot 0.14
12 HA202HYP HG 12   0.09  1.008   ;
qtot 0.23
13CP3202HYP CD 13  0 12.011   ;
qtot 0.23
14 HA202HYP   HD21 14   0.09  1.008   ;
qtot 0.32
15 HA202HYP   HD22 15   0.09  1.008   ;
qtot 0.41
16OH1202HYPOD1 16  -0.66 15.999   ;
qtot -0.25
17  H202HYPHD1 17   0.43  1.008   ;
qtot 0.18



On Thu 10 May, 2018, 18:07 Justin Lemkul,  wrote:

>
>
> On 5/10/18 8:29 AM, Hemalatha Jayabal wrote:
> > Hi all,
> >
> > I have added a non standard amino acid 'Hydroxyproline' to my forcefield
> > (from literature) Charmm27 and after using pdb2gmx i could see that the
> > system has a non integer charge value for 1 protein chain out of 3
> protein
> > chains.  (All 3 chains contain the non standard amino acid)
> >   The problem is occuring in the chain in which the terminal residue is
> this
> > hydroxyproline. (All other places where the 'HYP' residue appears, the
> > charge is 0). I tried using different terminii just to be sure that the
> > problem is not because of the terminii.
> >
> > What should be done in such a case?
>
> That depends on if the magnitude of the charge is meaningful or not. If
> you have two "correct" chains and one "incorrect" chain, that suggests
> that nothing is likely wrong with your HYP residue so things should be
> fine, but refer to
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic to be
> sure. The current version of GROMACS (2018.1) handles these rounding
> issues better to trigger fewer false warnings.
>
> -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.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] Non integer charge value

[Justin Lemkul]

On 5/10/18 8:29 AM, Hemalatha Jayabal wrote:

Hi all,

I have added a non standard amino acid 'Hydroxyproline' to my forcefield
(from literature) Charmm27 and after using pdb2gmx i could see that the
system has a non integer charge value for 1 protein chain out of 3 protein
chains.  (All 3 chains contain the non standard amino acid)
  The problem is occuring in the chain in which the terminal residue is this
hydroxyproline. (All other places where the 'HYP' residue appears, the
charge is 0). I tried using different terminii just to be sure that the
problem is not because of the terminii.

What should be done in such a case?


That depends on if the magnitude of the charge is meaningful or not. If 
you have two "correct" chains and one "incorrect" chain, that suggests 
that nothing is likely wrong with your HYP residue so things should be 
fine, but refer to 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic to be 
sure. The current version of GROMACS (2018.1) handles these rounding 
issues better to trigger fewer false warnings.


-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.thelemkullab.com

==

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[gmx-users] Non integer charge value

[Hemalatha Jayabal]

Hi all,

I have added a non standard amino acid 'Hydroxyproline' to my forcefield
(from literature) Charmm27 and after using pdb2gmx i could see that the
system has a non integer charge value for 1 protein chain out of 3 protein
chains.  (All 3 chains contain the non standard amino acid)
 The problem is occuring in the chain in which the terminal residue is this
hydroxyproline. (All other places where the 'HYP' residue appears, the
charge is 0). I tried using different terminii just to be sure that the
problem is not because of the terminii.

What should be done in such a case?
-- 
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Re: [gmx-users] Rupture force definition

[Justin Lemkul]

On 5/10/18 8:17 AM, Rakesh Mishra wrote:

Thanks to ur quick response

Would you please shed some light on my query no. 1 about the box size.
Please go through that.


I don't know exactly what you'd like me to say. Your interpretation of 
GROMACS' requirements is correct. I don't know what other software does 
in this context. Use whatever you like, but be sure you are not 
violating the minimum image convention in whatever program you use.


-Justin


On Thu, May 10, 2018 at 5:35 PM, Justin Lemkul  wrote:



On 5/10/18 1:24 AM, Rakesh Mishra wrote:


Dear Justin,

I have discussed a lot regarding the pulling of dsRNA/dsDNA using gromacs
about your protocol. Thanks for  those discussion.
But  I faced two more basic problem in gromacs.

1-   I need double size box if I need to pull half distance of box (Which
makes time demanding ).
Eg.  let I want to pull DNA of length 34 Angstroms (3.4 nm) to 68
Angstroms (6.8 nm) along X direction.
Then I need to make the box of the  size just double of 6.8 nm i.e
we need to box that must be extended in the pulling direction of the size
13. 6 nm.
And then it needs lots of time to simulate compare to if I use
other
simulation tool for  pulling like NAMD or Amber, where no need to make the
box size double
then the given pulling distance. Then  Why Gromacs should be used
for
pulling .


Use whatever software you like. No one says you have to use GROMACS :)

2-  And I use constant velocity pulling with distance increasing. Then Its

not possible to get variation of force/distance . It just gives linear
variation like straight line with force.
   Yes, it gives basically variation of force with the time .


Forces are in pullf.xvg and the displacement is in pullx.xvg. You can
easily plot force vs. distance from these two files.

3-  But suppose we want get force versus stretch(extension) curve then how

to do constant force pulling like constant velocity.


There is an option of constant force pulling you can set in the .mdp file,
but it won't be useful to plot force vs. displacement/extension in this
case because the force is, by definition, constant.



4-  Should we use NAMD for simple force versus extension curve .


NAMD can do this kind of simulation if you prefer, but you can certainly
do it with GROMACS.

-Justin

 My above 1-2-3 questions are important for me as a gromacs user.  If

possible please ans, I will be great full to you.



On Fri, Feb 16, 2018 at 12:40 PM, Rakesh Mishra 
wrote:

Dear Justin thanks for detail.

Initially my system was positioned along the x direction. final
structure,
that we got After 10 ns generation for pulling
that system is slightly tilts toward the z direction but not exactly.
Please find the attache snapshot of tilted picture.
In this picture, I am trying to pull the left side end (in the downward z
direction),which is close to the z axis.



On Thu, Feb 15, 2018 at 7:04 PM, Justin Lemkul  wrote:



On 2/15/18 4:13 AM, Rakesh Mishra wrote:

Dear Justin thanks for your advise.

I will check for longer run for getting response according to you.


I would like to explain my system,which is siRNA of chain A and B.
Here, after doing all formalities, I had run 10 ns then try to apply
the
pull protocol.

See, here for pulling this system, I have restricted 1st residue of
chain-A, and pulling last ( 22th)
residue of chain-B, which is at the same side end just below the 1st
residue of chain-A.
( means, both reference and pull groups are at the same end side ).

Note- I am pulling this 22th residue of chain-B in the downward (-z)
direction with negative rate.
( here pull group is below from the reference group)

I also  followed your advise to pull with negative rate with high
spring
constant. But  in this case also,
system is not moving in the downwards (-z  ) direction.

Interesting-
But the most interesting case is that for the same system just
discussed
above, when I am
applying pulling code with + rate even with smaller spring constant,
then
system is moving in
downward (-z) direction. While In my thinking, because I have given
+rate,
so it should move in
the + z direction. So, could it be possible that there is one thing
that
can also matter ,
i.e. whether, pull group is below and reference group is above .

Because in the same system, when I pull 22the residue of chain-A w.r.t
reference residue 1 of chain-B
(which is slightly below from the pull residue 22th of chain-A) with
the
same +rate and spring constant.
In this case pull group moves in the + z direction (upward), which I
expect
( note-  here pull group is
slightly above from the reference group)

So, this contradiction with effect based on the end side pulling and
posing
of reference and pull groups
is making it surprise and trouble.

How is the RNA oriented? Is the z-axis coincident with the helical

axis?
If so, that's a poor choice for a reaction coordinate and you 

Re: [gmx-users] Rupture force definition

[Rakesh Mishra]

Thanks to ur quick response

Would you please shed some light on my query no. 1 about the box size.
Please go through that.

On Thu, May 10, 2018 at 5:35 PM, Justin Lemkul  wrote:

>
>
> On 5/10/18 1:24 AM, Rakesh Mishra wrote:
>
>> Dear Justin,
>>
>> I have discussed a lot regarding the pulling of dsRNA/dsDNA using gromacs
>> about your protocol. Thanks for  those discussion.
>> But  I faced two more basic problem in gromacs.
>>
>> 1-   I need double size box if I need to pull half distance of box (Which
>> makes time demanding ).
>>Eg.  let I want to pull DNA of length 34 Angstroms (3.4 nm) to 68
>> Angstroms (6.8 nm) along X direction.
>>Then I need to make the box of the  size just double of 6.8 nm i.e
>> we need to box that must be extended in the pulling direction of the size
>> 13. 6 nm.
>>And then it needs lots of time to simulate compare to if I use
>> other
>> simulation tool for  pulling like NAMD or Amber, where no need to make the
>> box size double
>>then the given pulling distance. Then  Why Gromacs should be used
>> for
>> pulling .
>>
>
> Use whatever software you like. No one says you have to use GROMACS :)
>
> 2-  And I use constant velocity pulling with distance increasing. Then Its
>> not possible to get variation of force/distance . It just gives linear
>> variation like straight line with force.
>>   Yes, it gives basically variation of force with the time .
>>
>
> Forces are in pullf.xvg and the displacement is in pullx.xvg. You can
> easily plot force vs. distance from these two files.
>
> 3-  But suppose we want get force versus stretch(extension) curve then how
>> to do constant force pulling like constant velocity.
>>
>
> There is an option of constant force pulling you can set in the .mdp file,
> but it won't be useful to plot force vs. displacement/extension in this
> case because the force is, by definition, constant.
>
>
>> 4-  Should we use NAMD for simple force versus extension curve .
>>
>
> NAMD can do this kind of simulation if you prefer, but you can certainly
> do it with GROMACS.
>
> -Justin
>
> My above 1-2-3 questions are important for me as a gromacs user.  If
>> possible please ans, I will be great full to you.
>>
>>
>>
>> On Fri, Feb 16, 2018 at 12:40 PM, Rakesh Mishra 
>> wrote:
>>
>> Dear Justin thanks for detail.
>>>
>>> Initially my system was positioned along the x direction. final
>>> structure,
>>> that we got After 10 ns generation for pulling
>>> that system is slightly tilts toward the z direction but not exactly.
>>> Please find the attache snapshot of tilted picture.
>>> In this picture, I am trying to pull the left side end (in the downward z
>>> direction),which is close to the z axis.
>>>
>>>
>>>
>>> On Thu, Feb 15, 2018 at 7:04 PM, Justin Lemkul  wrote:
>>>
>>>
 On 2/15/18 4:13 AM, Rakesh Mishra wrote:

 Dear Justin thanks for your advise.
>
> I will check for longer run for getting response according to you.
>
>
> I would like to explain my system,which is siRNA of chain A and B.
> Here, after doing all formalities, I had run 10 ns then try to apply
> the
> pull protocol.
>
> See, here for pulling this system, I have restricted 1st residue of
> chain-A, and pulling last ( 22th)
> residue of chain-B, which is at the same side end just below the 1st
> residue of chain-A.
> ( means, both reference and pull groups are at the same end side ).
>
> Note- I am pulling this 22th residue of chain-B in the downward (-z)
> direction with negative rate.
>( here pull group is below from the reference group)
>
> I also  followed your advise to pull with negative rate with high
> spring
> constant. But  in this case also,
> system is not moving in the downwards (-z  ) direction.
>
> Interesting-
> But the most interesting case is that for the same system just
> discussed
> above, when I am
> applying pulling code with + rate even with smaller spring constant,
> then
> system is moving in
> downward (-z) direction. While In my thinking, because I have given
> +rate,
> so it should move in
> the + z direction. So, could it be possible that there is one thing
> that
> can also matter ,
> i.e. whether, pull group is below and reference group is above .
>
> Because in the same system, when I pull 22the residue of chain-A w.r.t
> reference residue 1 of chain-B
> (which is slightly below from the pull residue 22th of chain-A) with
> the
> same +rate and spring constant.
> In this case pull group moves in the + z direction (upward), which I
> expect
> ( note-  here pull group is
> slightly above from the reference group)
>
> So, this contradiction with effect based on the end side pulling and
> posing
> of reference and pull groups
> is making 

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

On 5/10/18 7:08 AM, neelam wafa wrote:

Hi gmx users!

I am running a 5ns md simmulation of a protein with 250 steps. It
crashed at  136 steps due to some power problem. Now I want to continue
this simmulation. In the manual following command is given:

mdrun -s topol.tpr -cpi state.cpt

but I am confused which file is state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?


Look at the time stamps of the files and inspect their contents with gmx 
check. You will see an obvious difference in what they contain. Also 
consult the mdrun help info, which specifically addresses your question.



Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?


Yes, because that file is only produced from the last step.


Also do I need to specify  -append flag or not? I am using version 5.1.5


-append has been the default option for many years. Again, see the mdrun 
help description.


-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.thelemkullab.com

==

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Re: [gmx-users] Improper dihedrals ordering issue

[Justin Lemkul]

On 5/10/18 2:56 AM, Hemalatha Jayabal wrote:

Hi all,

I am a beginner in GROMACS. I have a protein in which there is a non
standard amino acid for which parameters are added manually by me from
literature. I am using CHARMM27 force field in GROMACS. I got the topology
by using pdb2gmx. While adding ions to make my system neutral I encountered
an error saying that improper dihedral parameters were not found. On
looking onto the dihedrals, i found that the central atom was 'k' and not
'i' (like the standard gromacs dihedrals). When i checked other dihedrals
without the manually added residue, the central atom was 'i'.

I am confused as to whether the dihedral parameters from ffbonded could be
re-ordered for this case and could be used. (The order mentioned in
topology but parameters for same dihedral in ffbonded)


Don't re-order existing parameters. Make the ones you have added conform 
to the required format.


-Justin

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Assistant Professor
Virginia Tech Department of Biochemistry

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Re: [gmx-users] Rupture force definition

[Justin Lemkul]

On 5/10/18 1:24 AM, Rakesh Mishra wrote:

Dear Justin,

I have discussed a lot regarding the pulling of dsRNA/dsDNA using gromacs
about your protocol. Thanks for  those discussion.
But  I faced two more basic problem in gromacs.

1-   I need double size box if I need to pull half distance of box (Which
makes time demanding ).
   Eg.  let I want to pull DNA of length 34 Angstroms (3.4 nm) to 68
Angstroms (6.8 nm) along X direction.
   Then I need to make the box of the  size just double of 6.8 nm i.e
we need to box that must be extended in the pulling direction of the size
13. 6 nm.
   And then it needs lots of time to simulate compare to if I use other
simulation tool for  pulling like NAMD or Amber, where no need to make the
box size double
   then the given pulling distance. Then  Why Gromacs should be used for
pulling .


Use whatever software you like. No one says you have to use GROMACS :)


2-  And I use constant velocity pulling with distance increasing. Then Its
not possible to get variation of force/distance . It just gives linear
variation like straight line with force.
  Yes, it gives basically variation of force with the time .


Forces are in pullf.xvg and the displacement is in pullx.xvg. You can 
easily plot force vs. distance from these two files.



3-  But suppose we want get force versus stretch(extension) curve then how
to do constant force pulling like constant velocity.


There is an option of constant force pulling you can set in the .mdp 
file, but it won't be useful to plot force vs. displacement/extension in 
this case because the force is, by definition, constant.




4-  Should we use NAMD for simple force versus extension curve .


NAMD can do this kind of simulation if you prefer, but you can certainly 
do it with GROMACS.


-Justin


My above 1-2-3 questions are important for me as a gromacs user.  If
possible please ans, I will be great full to you.



On Fri, Feb 16, 2018 at 12:40 PM, Rakesh Mishra  wrote:


Dear Justin thanks for detail.

Initially my system was positioned along the x direction. final structure,
that we got After 10 ns generation for pulling
that system is slightly tilts toward the z direction but not exactly.
Please find the attache snapshot of tilted picture.
In this picture, I am trying to pull the left side end (in the downward z
direction),which is close to the z axis.



On Thu, Feb 15, 2018 at 7:04 PM, Justin Lemkul  wrote:



On 2/15/18 4:13 AM, Rakesh Mishra wrote:


Dear Justin thanks for your advise.

I will check for longer run for getting response according to you.


I would like to explain my system,which is siRNA of chain A and B.
Here, after doing all formalities, I had run 10 ns then try to apply the
pull protocol.

See, here for pulling this system, I have restricted 1st residue of
chain-A, and pulling last ( 22th)
residue of chain-B, which is at the same side end just below the 1st
residue of chain-A.
( means, both reference and pull groups are at the same end side ).

Note- I am pulling this 22th residue of chain-B in the downward (-z)
direction with negative rate.
   ( here pull group is below from the reference group)

I also  followed your advise to pull with negative rate with high spring
constant. But  in this case also,
system is not moving in the downwards (-z  ) direction.

Interesting-
But the most interesting case is that for the same system just discussed
above, when I am
applying pulling code with + rate even with smaller spring constant, then
system is moving in
downward (-z) direction. While In my thinking, because I have given
+rate,
so it should move in
the + z direction. So, could it be possible that there is one thing that
can also matter ,
i.e. whether, pull group is below and reference group is above .

Because in the same system, when I pull 22the residue of chain-A w.r.t
reference residue 1 of chain-B
(which is slightly below from the pull residue 22th of chain-A) with the
same +rate and spring constant.
In this case pull group moves in the + z direction (upward), which I
expect
( note-  here pull group is
slightly above from the reference group)

So, this contradiction with effect based on the end side pulling and
posing
of reference and pull groups
is making it surprise and trouble.


How is the RNA oriented? Is the z-axis coincident with the helical axis?
If so, that's a poor choice for a reaction coordinate and you should choose
a different axis, orthogonal to the helix. Or just pull in all dimensions
so that it's the total COM distance between the base pair. Remember, the
tutorial is a special case in which a one-dimension pull made sense due to
the inherent geometry of the unidirectional growth model of amyloid
fibrils. Do not assume that all system should be treated this way.

The negative pull rate means "bring the two specified groups together"
not necessarily "pull along -z" so be sure your orientation convention
aligns with what 

[gmx-users] Restarting crashed simmulation.

[neelam wafa]

Hi gmx users!

I am running a 5ns md simmulation of a protein with 250 steps. It
crashed at  136 steps due to some power problem. Now I want to continue
this simmulation. In the manual following command is given:

mdrun -s topol.tpr -cpi state.cpt

but I am confused which file is state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?

Also do I need to specify  -append flag or not? I am using version 5.1.5

Please need urgent answer.
Regards
Neelam Wafa
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[gmx-users] Improper dihedrals ordering issue

[Hemalatha Jayabal]

Hi all,

I am a beginner in GROMACS. I have a protein in which there is a non
standard amino acid for which parameters are added manually by me from
literature. I am using CHARMM27 force field in GROMACS. I got the topology
by using pdb2gmx. While adding ions to make my system neutral I encountered
an error saying that improper dihedral parameters were not found. On
looking onto the dihedrals, i found that the central atom was 'k' and not
'i' (like the standard gromacs dihedrals). When i checked other dihedrals
without the manually added residue, the central atom was 'i'.

I am confused as to whether the dihedral parameters from ffbonded could be
re-ordered for this case and could be used. (The order mentioned in
topology but parameters for same dihedral in ffbonded)

I hope I am clear regarding my query

Regards
Hemalatha Jayabal
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