Re: [gmx-users] Problem with my pull-code or my topology (or both) - help appreciated

[Justin Lemkul]

On 8/8/16 5:00 PM, Billy Williams-Noonan wrote:

Hi Justin,

Thank you for the confirmation that the pull-code is doing what I thought.
:)

My confusion is in the fact that the stability of my system seemed to
depend largely on what cluster I used.

If I used this one:
http://www.synchrotron.org.au/about-us/our-facilities/scientific-computing-a-it/massive

Every umbrella window of my system crashed within 200 ps, generating over
1000 LINCS warnings.

But if I did the same thing (no changes) on this cluster (Snowy):
https://www.vlsci.org.au/page/computer-software-configuration.

Everything runs stably.

And there are never any LINCS warning on the local machines we have either,
where I simply pull the ligand into position over 400ps, but what I'm
finding is that sometimes the ligand never moves to the specified COM pull
distance even with the high force constant, but when I re-equilibrate my
ensemble it usually does...

Hope that helps explain my confusion...



Any number of things could be wrong here.  Do all the GROMACS tests pass on all 
architectures?  Are the compilers, MPI libraries, etc. all free from bugs? 
You'll often find considerable variability across different clusters, and not 
all sysadmins are created equal :)  There are plenty of buggy things completely 
outside GROMACS that could be to blame, but with only this information, it's 
like shooting in the dark.


-Justin


Best regards,

Billy

On 8 August 2016 at 20:05, Justin Lemkul  wrote:




On 8/7/16 7:33 PM, Billy Williams-Noonan wrote:


Hi All,

Just an update.  I regenerated the topology for the linear peptide with
the
ATB and found myself with similar problems.

Will this pull until the Z-component of the COM distance is 3.2 nm and
hold
it in place?

pull= yes

pull_ngroups= 2
pull_ncoords= 1
pull_coord1-groups  = 1 2
pull_group1_name= reference_pull_group
pull_group2_name= Pull_Group
pull_coord1-type= umbrella
pull_coord1-geometry= direction
pull_coord1-dim = N N Y
;pull_coord1-rate   = 0.5
pull_coord1-k   = 1000
pull_coord1-vec = 0 0 1
pull_coord1-init=  *3.20*
pull_coord1-start   = no

pull_print-components   = yes

pull_nstxout = 10
pull_nstfout = 1

Is this doing what I think it is doing?  Because it has worked for every
other example I have been using.



I just posted in a similar thread about this - in effect, yes, but if your
starting distance deviates a lot from 3.2, the initial forces are going to
be massive and potentially unstable.

-Justin

Best regards,


Billy

On 4 August 2016 at 17:28, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

Hi Gromacs Users,


I have been pulling peptides from two separate proteins (let's call them
A
and B) by first taking the crystal structure pose and pulling the ligand
to
progressively more distant points from the binding site, and then
sampling
at that point.

I first pull the ligand out of the binding site over 400ps with a high
force constant (1 kJ/mol/nm^2), and then sample at that point with a
lower force constant (1000 kJ/mol/nm^2)

The pull-code I have been using in my .mdp file is this:

*400 ps Pull*

pull= yes

pull_ngroups= 2
pull_ncoords= 1
pull_coord1-groups  = 1 2
pull_group1_name= reference_pull_group
pull_group2_name= Pull_Group
pull_coord1-type= umbrella
pull_coord1-geometry= direction
pull_coord1-dim = N N Y
pull_coord1-k   = 2
pull_coord1-vec = 0 0 1
pull_coord1-init=* pull-distance  *
pull_coord1-start   = no

pull_print-components   = yes

pull_nstxout = 10
pull_nstfout = 1

*20 ns sampling:  *

pull= yes

pull_ngroups= 2
pull_ncoords= 1
pull_coord1-groups  = 1 2
pull_group1_name= reference_pull_group
pull_group2_name= Pull_Group
pull_coord1-type= umbrella
pull_coord1-geometry= direction
pull_coord1-dim = N N Y
;pull_coord1-rate   = 0.5
pull_coord1-k   = 1000
pull_coord1-vec = 0 0 1
pull_coord1-init=  *pull-distance*
pull_coord1-start   = no

pull_print-components   = yes

pull_nstxout = 10
pull_nstfout = 1

This has worked for two ligands binding to A and one ligand binding to B
with varying degrees of agreement with experiment.

However, when I try to move my ligands into position with one
linear-peptide ligand binding to B, the ligand moves to 2.7 nm between
the
two pull-group's COM... and then refuses to move further.  The initial
COM
pull distance was 1.8 nm, and the final pull distance should be 3.2 nm
between the two pull groups' COM.

A cyclic peptide version of this molecule was pulled from the binding
site
successfully and its topology was generated with the ATB. The linear
version of this peptide was generated with gmx pdb2gmx and this is the
*only* difference in 

Re: [gmx-users] Install Problem: make check, tests failed, incompatible library version

[Justin Lemkul]

On 8/8/16 1:35 PM, Betty Wong wrote:

Hi,

Posting again, hoping someone will help me! Much appreciated.

I am trying to install Gromacs. (I believe that) I have successfully done
the following:

tar xfz gromacs-5.1.3.tar.gz
cd gromacs-5.1.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make


But when I get to make check, I get an error, I've copied and pasted only
one part of the what error output is.
 Start 20: MdrunMpiTests

20/26 Test #20: MdrunMpiTests ***Exception: Other  0.02
sec

dyld: Library not loaded: libxml2.2.dylib

  Referenced from: /Users/bwong/Desktop/gromacs-
5.1.3/build/bin/mdrun-mpi-test

  Reason: Incompatible library version: mdrun-mpi-test requires version
12.0.0 or later, but libxml2.2.dylib provides version 10.0.0



You need to upgrade to a newer version for this to work.

-Justin


And if this helps as well:

The following tests FAILED:

  1 - TestUtilsUnitTests (OTHER_FAULT)

  2 - GmxlibTests (OTHER_FAULT)

  3 - MdlibUnitTest (OTHER_FAULT)

  4 - CommandLineUnitTests (OTHER_FAULT)

  5 - FFTUnitTests (OTHER_FAULT)

  6 - MathUnitTests (OTHER_FAULT)

  7 - RandomUnitTests (OTHER_FAULT)

  8 - OnlineHelpUnitTests (OTHER_FAULT)

  9 - OptionsUnitTests (OTHER_FAULT)

10 - UtilityUnitTests (OTHER_FAULT)

11 - FileIOTests (OTHER_FAULT)

12 - SimdUnitTests (OTHER_FAULT)

13 - LegacyToolsTests (OTHER_FAULT)

14 - GmxPreprocessTests (OTHER_FAULT)

15 - CorrelationsTest (OTHER_FAULT)

16 - AnalysisDataUnitTests (OTHER_FAULT)

17 - SelectionUnitTests (OTHER_FAULT)

18 - TrajectoryAnalysisUnitTests (OTHER_FAULT)

19 - MdrunTests (OTHER_FAULT)

20 - MdrunMpiTests (OTHER_FAULT)

Errors while running CTest

make[3]: *** [CMakeFiles/run-ctest] Error 8

make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2

make[1]: *** [CMakeFiles/check.dir/rule] Error 2

make: *** [check] Error 2

Any help? Not sure what the error is and how to fix. Thanks!

Best,
Betty



--
==

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] Defining a limited space for the movement of Ion

[Justin Lemkul]

On 8/8/16 9:31 AM, Alexander Alexander wrote:

Thanks for your suggestions.

Can you please confirm me that the reference position in the spherical
flat-bottom restraint should be defined in a separated file passing by "-r"
from grompp. Since I want that the Ion accompanies the molecule in the


Yes.


whole simulation, then I was wondering if this reference position also is
allowed to move(sphere also moves) as well or it is just a fix position as
center of sphere? How can I make a relation between this reference position
and molecule?



The reference position is the coordinates themselves, scaled by refcoord_scaling 
if using pressure coupling.  If the protein drifts significantly over the course 
of the simulation, this may not achieve what you want, without an additional 
restraint on protein COM motion (which can also be done).



If I want to use the pull code to do so, I was wondering how tight the
spring should be (the force constant) approximately?



No idea offhand.  There are no hard rules here.

-Justin


Thanks,
Regards,
Alex

On Mon, Aug 8, 2016 at 1:46 PM, Justin Lemkul  wrote:




On 8/8/16 7:10 AM, Alexander Alexander wrote:


Dear Gromacs user,

I have defined a "molecule = A" and a single ion together as
"[moleculetype] = A + Ion" in my simulations. But, I get some problem when
Ion goes so far away from the molecule A, because physically I would have
a
separated molecules defined as [moleculetype], so, I want somehow keep the
Ion close to the molecule in simulation, I mean just in physically
meaningful-limited sphere around the the molecule.
Would you please let me know how I can do that?



Use either the pull code or a spherical flat-bottom restraint on the ion.

-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

==
--
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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send a mail to gmx-users-requ...@gromacs.org.



--
==

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

==
--
Gromacs Users mailing list

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Problem with my pull-code or my topology (or both) - help appreciated

[Billy Williams-Noonan]

Hi Justin,

Thank you for the confirmation that the pull-code is doing what I thought.
:)

My confusion is in the fact that the stability of my system seemed to
depend largely on what cluster I used.

If I used this one:
http://www.synchrotron.org.au/about-us/our-facilities/scientific-computing-a-it/massive

Every umbrella window of my system crashed within 200 ps, generating over
1000 LINCS warnings.

But if I did the same thing (no changes) on this cluster (Snowy):
https://www.vlsci.org.au/page/computer-software-configuration.

Everything runs stably.

And there are never any LINCS warning on the local machines we have either,
where I simply pull the ligand into position over 400ps, but what I'm
finding is that sometimes the ligand never moves to the specified COM pull
distance even with the high force constant, but when I re-equilibrate my
ensemble it usually does...

Hope that helps explain my confusion...

Best regards,

Billy

On 8 August 2016 at 20:05, Justin Lemkul  wrote:

>
>
> On 8/7/16 7:33 PM, Billy Williams-Noonan wrote:
>
>> Hi All,
>>
>> Just an update.  I regenerated the topology for the linear peptide with
>> the
>> ATB and found myself with similar problems.
>>
>> Will this pull until the Z-component of the COM distance is 3.2 nm and
>> hold
>> it in place?
>>
>> pull= yes
>>
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_coord1-groups  = 1 2
>> pull_group1_name= reference_pull_group
>> pull_group2_name= Pull_Group
>> pull_coord1-type= umbrella
>> pull_coord1-geometry= direction
>> pull_coord1-dim = N N Y
>> ;pull_coord1-rate   = 0.5
>> pull_coord1-k   = 1000
>> pull_coord1-vec = 0 0 1
>> pull_coord1-init=  *3.20*
>> pull_coord1-start   = no
>>
>> pull_print-components   = yes
>>
>> pull_nstxout = 10
>> pull_nstfout = 1
>>
>> Is this doing what I think it is doing?  Because it has worked for every
>> other example I have been using.
>>
>>
> I just posted in a similar thread about this - in effect, yes, but if your
> starting distance deviates a lot from 3.2, the initial forces are going to
> be massive and potentially unstable.
>
> -Justin
>
> Best regards,
>>
>> Billy
>>
>> On 4 August 2016 at 17:28, Billy Williams-Noonan <
>> billy.williams-noo...@monash.edu> wrote:
>>
>> Hi Gromacs Users,
>>>
>>> I have been pulling peptides from two separate proteins (let's call them
>>> A
>>> and B) by first taking the crystal structure pose and pulling the ligand
>>> to
>>> progressively more distant points from the binding site, and then
>>> sampling
>>> at that point.
>>>
>>> I first pull the ligand out of the binding site over 400ps with a high
>>> force constant (1 kJ/mol/nm^2), and then sample at that point with a
>>> lower force constant (1000 kJ/mol/nm^2)
>>>
>>> The pull-code I have been using in my .mdp file is this:
>>>
>>> *400 ps Pull*
>>>
>>> pull= yes
>>>
>>> pull_ngroups= 2
>>> pull_ncoords= 1
>>> pull_coord1-groups  = 1 2
>>> pull_group1_name= reference_pull_group
>>> pull_group2_name= Pull_Group
>>> pull_coord1-type= umbrella
>>> pull_coord1-geometry= direction
>>> pull_coord1-dim = N N Y
>>> pull_coord1-k   = 2
>>> pull_coord1-vec = 0 0 1
>>> pull_coord1-init=* pull-distance  *
>>> pull_coord1-start   = no
>>>
>>> pull_print-components   = yes
>>>
>>> pull_nstxout = 10
>>> pull_nstfout = 1
>>>
>>> *20 ns sampling:  *
>>>
>>> pull= yes
>>>
>>> pull_ngroups= 2
>>> pull_ncoords= 1
>>> pull_coord1-groups  = 1 2
>>> pull_group1_name= reference_pull_group
>>> pull_group2_name= Pull_Group
>>> pull_coord1-type= umbrella
>>> pull_coord1-geometry= direction
>>> pull_coord1-dim = N N Y
>>> ;pull_coord1-rate   = 0.5
>>> pull_coord1-k   = 1000
>>> pull_coord1-vec = 0 0 1
>>> pull_coord1-init=  *pull-distance*
>>> pull_coord1-start   = no
>>>
>>> pull_print-components   = yes
>>>
>>> pull_nstxout = 10
>>> pull_nstfout = 1
>>>
>>> This has worked for two ligands binding to A and one ligand binding to B
>>> with varying degrees of agreement with experiment.
>>>
>>> However, when I try to move my ligands into position with one
>>> linear-peptide ligand binding to B, the ligand moves to 2.7 nm between
>>> the
>>> two pull-group's COM... and then refuses to move further.  The initial
>>> COM
>>> pull distance was 1.8 nm, and the final pull distance should be 3.2 nm
>>> between the two pull groups' COM.
>>>
>>> A cyclic peptide version of this molecule was pulled from the binding
>>> site
>>> successfully and its topology was generated with the ATB. The linear
>>> version of this peptide was generated with gmx pdb2gmx and this is the
>>> *only* difference in the protocol between the two protocols.
>>>
>>> So either the pull-code I 

[gmx-users] Install Problem: make check, tests failed, incompatible library version

[Betty Wong]

Hi,

Posting again, hoping someone will help me! Much appreciated.

I am trying to install Gromacs. (I believe that) I have successfully done
the following:

tar xfz gromacs-5.1.3.tar.gz
cd gromacs-5.1.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make


But when I get to make check, I get an error, I've copied and pasted only
one part of the what error output is.
 Start 20: MdrunMpiTests

20/26 Test #20: MdrunMpiTests ***Exception: Other  0.02
sec

dyld: Library not loaded: libxml2.2.dylib

  Referenced from: /Users/bwong/Desktop/gromacs-
5.1.3/build/bin/mdrun-mpi-test

  Reason: Incompatible library version: mdrun-mpi-test requires version
12.0.0 or later, but libxml2.2.dylib provides version 10.0.0

And if this helps as well:

The following tests FAILED:

  1 - TestUtilsUnitTests (OTHER_FAULT)

  2 - GmxlibTests (OTHER_FAULT)

  3 - MdlibUnitTest (OTHER_FAULT)

  4 - CommandLineUnitTests (OTHER_FAULT)

  5 - FFTUnitTests (OTHER_FAULT)

  6 - MathUnitTests (OTHER_FAULT)

  7 - RandomUnitTests (OTHER_FAULT)

  8 - OnlineHelpUnitTests (OTHER_FAULT)

  9 - OptionsUnitTests (OTHER_FAULT)

10 - UtilityUnitTests (OTHER_FAULT)

11 - FileIOTests (OTHER_FAULT)

12 - SimdUnitTests (OTHER_FAULT)

13 - LegacyToolsTests (OTHER_FAULT)

14 - GmxPreprocessTests (OTHER_FAULT)

15 - CorrelationsTest (OTHER_FAULT)

16 - AnalysisDataUnitTests (OTHER_FAULT)

17 - SelectionUnitTests (OTHER_FAULT)

18 - TrajectoryAnalysisUnitTests (OTHER_FAULT)

19 - MdrunTests (OTHER_FAULT)

20 - MdrunMpiTests (OTHER_FAULT)

Errors while running CTest

make[3]: *** [CMakeFiles/run-ctest] Error 8

make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2

make[1]: *** [CMakeFiles/check.dir/rule] Error 2

make: *** [check] Error 2

Any help? Not sure what the error is and how to fix. Thanks!

Best,
Betty
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Dan Gil]

I see. Now I understand what "pull-start" option means. Changing that
option made it work! Thank you Justin.

On Mon, Aug 8, 2016 at 6:04 AM, Justin Lemkul  wrote:

>
>
> On 8/7/16 1:21 PM, Dan Gil wrote:
>
>> In Gromacs/4.6, I used init to define the distance from the solvent COM
>> that the solute should be pulled to. Has it changed for Gromacs/5.1?
>>
>>
> Nothing has changed except (1) syntax and (2) the ability to now apply
> multiple restraints simultaneously.  Everything with respect to setting
> references distances, etc. is functionally the same.
>
> What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
>> the solvent COM?
>>
>>
> You can do that with "pull-coord1-init = X" and "pull-start = no" but this
> is setting the reference distance to X, so if the initial coordinates are
> far from that value, you're imparting a large force to start, which may not
> be stable. It may work, but those initial steps are going to be dicey.
>
> -Justin
>
>
> Here is the section I think you are talking about also:
>> Pull group 1 'a_Cooh' has 1 atoms
>> Pull group 2 'SOL' has 5715 atoms
>> Number of degrees of freedom in T-Coupling group System is 44530.00
>> Pull group  natoms  pbc atom  distance at start  reference at t=0
>>1 1 0
>>2  5715 18540   3.011 nm  3.011 nm
>>
>> On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 8/7/16 1:13 PM, Dan Gil wrote:
>>>
>>> Hi,

 I've made the change you suggested. The output file pullx.xvg has
 changed
 from something like:

 @ s0 legend "1"
 @ s1 legend "1 dZ"
 0. 3.01072 3.01072
 0.2000 2.98101 2.98101
 0.4000 2.94186 2.94186
 0.6000 2.95316 2.95316

 to this:

 @ s0 legend "1"
 @ s1 legend "1 dZ"
 0. 3.01072 -3.01072
 0.2000 2.98101 -2.98101
 0.4000 2.94186 -2.94186
 0.6000 2.95316 -2.95316

 The second column should the COM of the solvent, the third column should
 be
 the position of a_Cooh. I am still wondering what is going on, since
 init
 =
 0.



 pull-coord1-start= yes
>>>
>>> grompp tells you what the reference distance is at the start; check to
>>> make sure this is what you want it to be.  pull-coord1-init = 0 means
>>> "don't add anything extra to what is already there."
>>>
>>>
>>> -Justin
>>>
>>>
>>> On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul  wrote:



> On 8/7/16 11:35 AM, Dan Gil wrote:
>
> Hi,
>
>>
>> The pullx.xvg file is returning the coordinates of the solvent, and
>> not
>> the
>> solute (a_Cooh) as I want.
>> The solute is being pulled in a coordinate other than Z, although I
>> specify:
>>  pull-coord1-dim =N N Y
>> What is going on here?
>>
>>
>> Swap
>>
> pull-coord1-groups = 1 2
> for
> pull-coord1-groups = 2 1
>
> to do what you had been doing in the previous version.  You've inverted
> the pull vector relative to the 4.6 settings.
>
> -Justin
>
>
> On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
>
> billy.williams-noo...@monash.edu> wrote:
>>
>> Hi All,
>>
>>
>>> I'm having a similar problem and wouldn't mind some advice either.  I
>>> am
>>> getting LINCS warnings on one cluster that I run my sampling on, but
>>> the
>>> pull-code works fine on other clusters we have access to, which is
>>> making
>>> me doubt the entire process.
>>>
>>> Best regards,
>>>
>>> Billy
>>>
>>> On 7 August 2016 at 03:34, Dan Gil  wrote:
>>>
>>> Hi,
>>>
>>>
 I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
 .mdp
 file that I am confused with.

 I am pulling an atom of solute, indexed a_Cooh, towards the COM of

 solvent.

>>>
>>> This is a slab geometry, with the plane normal to the z-axis
>>> direction.
>>>

 My

>>>
>>> output (pullx.xvg) should contain the deltaZ value between the
>>> solute Z
>>>
 coordinate and solvent COM z coordinate. With my current Gromacs/5.1
 attempt, I don't think I am getting the correct results.

 On Gromacs/4.6:
 pull =umbrella
 pull_geometry =distance
 pull_dim =N N Y
 pull_init1 =0
 pull_k1 =100
 pull_nstxout =100
 pull_group0 =SOL
 pull_group1 =a_Cooh

 My attempt with Gromacs/5.1:
 pull =yes
 pull-ngroups= 2
 pull-ncoords= 1
 pull-group1-name = a_Cooh
 pull-group2-name = SOL
 pull-coord1-type  = umbrella
 pull-coord1-geometry =distance
 pull-coord1-groups = 1 2
 

Re: [gmx-users] Defining a limited space for the movement of Ion

[Alexander Alexander]

Thanks for your suggestions.

Can you please confirm me that the reference position in the spherical
flat-bottom restraint should be defined in a separated file passing by "-r"
from grompp. Since I want that the Ion accompanies the molecule in the
whole simulation, then I was wondering if this reference position also is
allowed to move(sphere also moves) as well or it is just a fix position as
center of sphere? How can I make a relation between this reference position
and molecule?

If I want to use the pull code to do so, I was wondering how tight the
spring should be (the force constant) approximately?

Thanks,
Regards,
Alex

On Mon, Aug 8, 2016 at 1:46 PM, Justin Lemkul  wrote:

>
>
> On 8/8/16 7:10 AM, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> I have defined a "molecule = A" and a single ion together as
>> "[moleculetype] = A + Ion" in my simulations. But, I get some problem when
>> Ion goes so far away from the molecule A, because physically I would have
>> a
>> separated molecules defined as [moleculetype], so, I want somehow keep the
>> Ion close to the molecule in simulation, I mean just in physically
>> meaningful-limited sphere around the the molecule.
>> Would you please let me know how I can do that?
>>
>>
> Use either the pull code or a spherical flat-bottom restraint on the ion.
>
> -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
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] Defining a limited space for the movement of Ion

[Justin Lemkul]

On 8/8/16 7:10 AM, Alexander Alexander wrote:

Dear Gromacs user,

I have defined a "molecule = A" and a single ion together as
"[moleculetype] = A + Ion" in my simulations. But, I get some problem when
Ion goes so far away from the molecule A, because physically I would have a
separated molecules defined as [moleculetype], so, I want somehow keep the
Ion close to the molecule in simulation, I mean just in physically
meaningful-limited sphere around the the molecule.
Would you please let me know how I can do that?



Use either the pull code or a spherical flat-bottom restraint on the ion.

-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] Defining a limited space for the movement of Ion

[Alexander Alexander]

Dear Gromacs user,

I have defined a "molecule = A" and a single ion together as
"[moleculetype] = A + Ion" in my simulations. But, I get some problem when
Ion goes so far away from the molecule A, because physically I would have a
separated molecules defined as [moleculetype], so, I want somehow keep the
Ion close to the molecule in simulation, I mean just in physically
meaningful-limited sphere around the the molecule.
Would you please let me know how I can do that?

Thanks,
Regards,
Alex
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[gmx-users] (no subject)

[hamedifatemeh67]

HiGROMACS users

Iam running mdrun and getting following error

 Fatalerror:

DD cell 0 0 3could only obtain 1065 of the 1066 atoms that are connected via 
constraintsfrom the neighboring cells. This probably means your constraint 
lengths are toolong compared to the domain decomposition cell size. Decrease 
the number ofdomain decomposition grid cells or lincs-order or use the -rcon 
option ofmdrun.

For solving this problem

(1)  In my mdp file lincs_order = 4 andlincs_iter =1 I got above error. I know 
if we don’t want to deteriorate thelincs accuracy (1+ lincs_iter)*lincs_order 
has to remain constant. So Idecreased lincs _order to (2) and increased 
lincs_iter to (3) proportionally.What I am following is right or I have 
misunderstood it. If so please correctit.

 (2)  According to the suggestionsfor trouble shooting of the error, I tried to 
decrease the number of grid cellsby option –dd but I don’t know what valus I 
should use with –dd! What is thedifference between –dd 118 and –dd 2 1 4?

   With the first one the run stoppedwhile with the other one it worked.

 (3)  Also I don’t know how can I use–rcon option?!  What value is 
appropriatefor –rcon?

Thanksin advance for your time

 

Sent from Yahoo Mail. Get the app
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Re: [gmx-users] Problem with my pull-code or my topology (or both) - help appreciated

[Justin Lemkul]

On 8/7/16 7:33 PM, Billy Williams-Noonan wrote:

Hi All,

Just an update.  I regenerated the topology for the linear peptide with the
ATB and found myself with similar problems.

Will this pull until the Z-component of the COM distance is 3.2 nm and hold
it in place?

pull= yes

pull_ngroups= 2
pull_ncoords= 1
pull_coord1-groups  = 1 2
pull_group1_name= reference_pull_group
pull_group2_name= Pull_Group
pull_coord1-type= umbrella
pull_coord1-geometry= direction
pull_coord1-dim = N N Y
;pull_coord1-rate   = 0.5
pull_coord1-k   = 1000
pull_coord1-vec = 0 0 1
pull_coord1-init=  *3.20*
pull_coord1-start   = no

pull_print-components   = yes

pull_nstxout = 10
pull_nstfout = 1

Is this doing what I think it is doing?  Because it has worked for every
other example I have been using.



I just posted in a similar thread about this - in effect, yes, but if your 
starting distance deviates a lot from 3.2, the initial forces are going to be 
massive and potentially unstable.


-Justin


Best regards,

Billy

On 4 August 2016 at 17:28, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:


Hi Gromacs Users,

I have been pulling peptides from two separate proteins (let's call them A
and B) by first taking the crystal structure pose and pulling the ligand to
progressively more distant points from the binding site, and then sampling
at that point.

I first pull the ligand out of the binding site over 400ps with a high
force constant (1 kJ/mol/nm^2), and then sample at that point with a
lower force constant (1000 kJ/mol/nm^2)

The pull-code I have been using in my .mdp file is this:

*400 ps Pull*

pull= yes

pull_ngroups= 2
pull_ncoords= 1
pull_coord1-groups  = 1 2
pull_group1_name= reference_pull_group
pull_group2_name= Pull_Group
pull_coord1-type= umbrella
pull_coord1-geometry= direction
pull_coord1-dim = N N Y
pull_coord1-k   = 2
pull_coord1-vec = 0 0 1
pull_coord1-init=* pull-distance  *
pull_coord1-start   = no

pull_print-components   = yes

pull_nstxout = 10
pull_nstfout = 1

*20 ns sampling:  *

pull= yes

pull_ngroups= 2
pull_ncoords= 1
pull_coord1-groups  = 1 2
pull_group1_name= reference_pull_group
pull_group2_name= Pull_Group
pull_coord1-type= umbrella
pull_coord1-geometry= direction
pull_coord1-dim = N N Y
;pull_coord1-rate   = 0.5
pull_coord1-k   = 1000
pull_coord1-vec = 0 0 1
pull_coord1-init=  *pull-distance*
pull_coord1-start   = no

pull_print-components   = yes

pull_nstxout = 10
pull_nstfout = 1

This has worked for two ligands binding to A and one ligand binding to B
with varying degrees of agreement with experiment.

However, when I try to move my ligands into position with one
linear-peptide ligand binding to B, the ligand moves to 2.7 nm between the
two pull-group's COM... and then refuses to move further.  The initial COM
pull distance was 1.8 nm, and the final pull distance should be 3.2 nm
between the two pull groups' COM.

A cyclic peptide version of this molecule was pulled from the binding site
successfully and its topology was generated with the ATB. The linear
version of this peptide was generated with gmx pdb2gmx and this is the
*only* difference in the protocol between the two protocols.

So either the pull-code I am using is not doing what I think it is
(pulling at specific distances along the Z-direction) *OR* the topology
being generated by *pdb2gmx* is wrong (but I don't think my input is
defective).  However, this would make sense given I am getting a lot of
LINCS warnings at some of my positions...

Specifically:


*WARNING (1):*
*lincs-warnangle can not be larger than 90 degrees, setting it to 90.*

Any help would be appreciated... :)

Best regards,

Billy...

--
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052







--
==

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] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Justin Lemkul]

On 8/7/16 1:21 PM, Dan Gil wrote:

In Gromacs/4.6, I used init to define the distance from the solvent COM
that the solute should be pulled to. Has it changed for Gromacs/5.1?



Nothing has changed except (1) syntax and (2) the ability to now apply multiple 
restraints simultaneously.  Everything with respect to setting references 
distances, etc. is functionally the same.



What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
the solvent COM?



You can do that with "pull-coord1-init = X" and "pull-start = no" but this is 
setting the reference distance to X, so if the initial coordinates are far from 
that value, you're imparting a large force to start, which may not be stable. 
It may work, but those initial steps are going to be dicey.


-Justin


Here is the section I think you are talking about also:
Pull group 1 'a_Cooh' has 1 atoms
Pull group 2 'SOL' has 5715 atoms
Number of degrees of freedom in T-Coupling group System is 44530.00
Pull group  natoms  pbc atom  distance at start  reference at t=0
   1 1 0
   2  5715 18540   3.011 nm  3.011 nm

On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul  wrote:




On 8/7/16 1:13 PM, Dan Gil wrote:


Hi,

I've made the change you suggested. The output file pullx.xvg has changed
from something like:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316

to this:

@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 -3.01072
0.2000 2.98101 -2.98101
0.4000 2.94186 -2.94186
0.6000 2.95316 -2.95316

The second column should the COM of the solvent, the third column should
be
the position of a_Cooh. I am still wondering what is going on, since init
=
0.




pull-coord1-start= yes

grompp tells you what the reference distance is at the start; check to
make sure this is what you want it to be.  pull-coord1-init = 0 means
"don't add anything extra to what is already there."


-Justin



On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul  wrote:




On 8/7/16 11:35 AM, Dan Gil wrote:

Hi,


The pullx.xvg file is returning the coordinates of the solvent, and not
the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I
specify:
 pull-coord1-dim =N N Y
What is going on here?


Swap

pull-coord1-groups = 1 2
for
pull-coord1-groups = 2 1

to do what you had been doing in the previous version.  You've inverted
the pull vector relative to the 4.6 settings.

-Justin


On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <


billy.williams-noo...@monash.edu> wrote:

Hi All,



I'm having a similar problem and wouldn't mind some advice either.  I
am
getting LINCS warnings on one cluster that I run my sampling on, but
the
pull-code works fine on other clusters we have access to, which is
making
me doubt the entire process.

Best regards,

Billy

On 7 August 2016 at 03:34, Dan Gil  wrote:

Hi,



I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of
.mdp
file that I am confused with.

I am pulling an atom of solute, indexed a_Cooh, towards the COM of

solvent.


This is a slab geometry, with the plane normal to the z-axis direction.


My


output (pullx.xvg) should contain the deltaZ value between the solute Z

coordinate and solvent COM z coordinate. With my current Gromacs/5.1
attempt, I don't think I am getting the correct results.

On Gromacs/4.6:
pull =umbrella
pull_geometry =distance
pull_dim =N N Y
pull_init1 =0
pull_k1 =100
pull_nstxout =100
pull_group0 =SOL
pull_group1 =a_Cooh

My attempt with Gromacs/5.1:
pull =yes
pull-ngroups= 2
pull-ncoords= 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type  = umbrella
pull-coord1-geometry =distance
pull-coord1-groups = 1 2
pull-coord1-dim =N N Y
pull-coord1-start= yes
pull-coord1-init  =0
pull-coord1-k=1000
pull-print-components = yes
pull_nstxout =100

Best Regards,

Dan
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*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] how likely that charmm-in-gromacs LJ-14 interactions are affected by inclusion of cgenff stuff when adding a new molecule with published charmm parameters?

[Justin Lemkul]

On 8/8/16 1:05 AM, Christopher Neale wrote:


Dear Justin:

I have another question, this time about LJ 1-4 interactions. I notice that
charmm36-jun2015.ff/ffbonded.itp has the following in [ pairtypes ]

NH1 S  1  0.316269044940  1.2552

and it has the following in [ atomtypes ]

S1632.060.000  A  0.356359487256  1.88280 NH1 7
14.0070000.000  A  0.329632525712  0.83680

charmm in gromacs is comb-rule 2, so sigma = aritmetic and epsilon =
geometric

For the S-NH1 LJ1-4 interaction, the epsilon makes sense, but the sigma is
off.

Am I to conclude from this that charmm uses a whole bunch of semi-arbitrary
LJ-14 terms? I checked in gromacs by simply removing the [ pairtypes ]
section and when I did that my energy match from gromacs to charmm executable
goes from not bad to really terrible (which aligns with the idea of charmm
having a bunch of pre-set 1-4 interactions).

My confusion stems from m reading of charmm mailing list posts in which alex
states that modifications of the LJ1-4 scaling is only done in special cases
(e.g,
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=1048 )



There are a few specific interactions that use special LJ 1-4 parameters.  What
is listed above is correct, because NH1 has a different Rmin/2 when in 1-4
interactions.  These parameters are explicitly listed in par_all36_prot.prm as
extra columns, as explained in the CHARMM documentation.  So these interactions
aren't "arbitrary" or hidden from the user, but you do have to know what you're
looking at.


I ask because I am trying to ensure that the inclusion of all the cgenff
stuff in the charmm36-jun2015.ff gromacs distribution is not going to
unexpectedly affect LJ1-4 interactions in a molecular modification for which
parameters have been published by another group who does their simulations
with charmm. In this case, my charmm vs gromacs executable LJ difference goes
up from ~ 0.01 kcal/mol for a 200 aa protein to 0.08 kcal/mol simply by
adding a ~10 heavy atom covalent acylation.



CGenFF and the parent CHARMM force field should be independent.  One should 
*not* be using CGenFF atom types for constituent residues of a protein, only 
noncovalent interactions like ligands, co-solvents, etc.  So CGenFF certainly 
will not affect 1-4 interactions in the protein.


You can verify the 1-4 vs. SR interactions in CHARMM with:

! list all 1-4 interactions and energies
! this actually returns 2*energy
coor dist ener cut 999. nononbonds noexclusions 14exclusions sele all end sele 
all end


! just the short-range energies
! likewise, 2*energy
coor dist ener cut 999. nonbonds noexclusions no14exclusions sele all end sele 
all end


This sometimes points to the nature of the underlying problem.

Without knowing exactly what you're trying to reproduce (what paper, what 
interactions, etc) there's not much more I can say.  Beware - some people play 
weird tricks that "work" but are not necessarily sensible.  This is why we keep 
very tight control over what actually gets integrated into the CHARMM force 
field.  The SI of some papers scares us...


-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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