[gmx-users] GMX_USE_RTD SCP=OFF CMAKE option

[Mehreen Jan]

> error:
> the gmx executable was compiled to use the rdtscp CPU
> instruction. however  this is not supported by the
> current hardware and continuing would ta a crash.please
> rebuild gromacs with GMX_USE_RTD SCP=OFF CMAKE option
> is it is installation issue???
> how to correct this issue???
> any ides??
> mehreen jan 
> 

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 78

[Mehreen Jan]

error:
the gmx executable was compiled to use the rdtscp CPU instruction. however  
this is not supported by the current hardware and continuing would ta a 
crash.please rebuild gromacs with GMX_USE_RTD SCP=OFF CMAKE option
is it is installation issue???
how to correct this issue???
any ides??
mehreen jan 


























On Mon, 15/2/16, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
 wrote:

 Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 78
 To: gromacs.org_gmx-users@maillist.sys.kth.se
 Received: Monday, 15 February, 2016, 10:14 PM
 
 Send gromacs.org_gmx-users mailing
 list submissions to
     gromacs.org_gmx-users@maillist.sys.kth.se
 
 To subscribe or unsubscribe via the World Wide Web, visit
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 When replying, please edit your Subject line so it is more
 specific
 than "Re: Contents of gromacs.org_gmx-users digest..."
 
 
 Today's Topics:
 
    1. Re: gromacs-5.1.1 installation error:
 libxml2 problem
       (Mark Abraham)
    2. Shrink simulation box while maintaining
 ensemble (Matthias Ernst)
    3. Re: gromacs-5.1.1 installation error:
 libxml2 problem
       (Irina Kosheleva)
    4. NVT-Eq ---> NVT-MD (Alexander
 Alexander)
    5. calculate *all* carbon atom distances
 over time? (Athina Meletiou)
    6. Re: NVT-Eq ---> NVT-MD (Justin
 Lemkul)
    7. Re: calculate *all* carbon atom
 distances over time?
       (Justin Lemkul)
 
 
 --
 
 Message: 1
 Date: Mon, 15 Feb 2016 15:29:32 +
 From: Mark Abraham 
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] gromacs-5.1.1 installation error:
 libxml2
     problem
 Message-ID:
     
 Content-Type: text/plain; charset=UTF-8
 
 Hi,
 
 Now that I have a computer again, I looked up what I did on
 Vesta, and in
 fact you don't need zlib support from libxml2, so just
 configure libxml2
 without that (and without python), and you'll be fine.
 
 I am also looking at how we can take this useless activity
 away from
 people...
 
 Mark
 
 
 --
 
 Message: 2
 Date: Mon, 15 Feb 2016 16:35:40 +0100
 From: Matthias Ernst 
 To: gmx-us...@gromacs.org
 Subject: [gmx-users] Shrink simulation box while maintaining
 ensemble
 Message-ID: <56c1f04c.90...@physik.uni-freiburg.de>
 Content-Type: text/plain; charset=utf-8
 
 Hi,
 
 I am running a protein folding simulation, starting with an
 extended
 structure that needs a lot of water molecules to fulfill the
 minimial
 image convenction.
 Is there a way to "shrink" a simulation box and get rid of
 unnecessary
 solvent molecules while keeping velocities (to preserve the
 ensemble as
 far as possible and avoid re-equilibration)?
 
 Thanks,
 Matthias
 
 -- 
 Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611
 
 
 --
 
 Message: 3
 Date: Mon, 15 Feb 2016 15:55:31 +
 From: Irina Kosheleva 
 To: "gmx-us...@gromacs.org"
 
 Subject: Re: [gmx-users] gromacs-5.1.1 installation error:
 libxml2
     problem
 Message-ID:
     
 Content-Type: text/plain; charset="us-ascii"
 
 Hi Mark,
 Thank you for your suggestions
 Indeed this works:
 For libxml2:
 ./configure
 --prefix=/home/ikosh/programs/autotools-bin 
 --without-python --without-zlib --without-lzma
 
 cmake -DCMAKE_C_COMPILER=mpixlc_r
 -DCMAKE_CXX_COMPILER=mpixlcxx_r
 -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C
 -DGMX_SIMD=IBM_QPX 
    -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF
 -DGMX_PREFER_STATIC_LIBS=ON  -DCMAKE_C_FLAGS="-O3
 -qsmp=omp -qarch=qp -qtune=qp"
 -DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
 -- Looking for NVIDIA GPUs present in the system
 
 -- Checking for MPI_IN_PLACE - yes
 -- Looking for zlibVersion in
 /home/ikosh/programs/autotools-bin/lib/libz.a
 -- Looking for zlibVersion in
 /home/ikosh/programs/autotools-bin/lib/libz.a - found
 -- Found LibXml2:
 /home/ikosh/programs/autotools-bin/lib/libxml2.a (found
 version "2.9.3") 
 -- Looking for xmlTextWriterEndAttribute in
 /home/ikosh/programs/autotools-bin/lib/libxml2.a
 -- Looking for xmlTextWriterEndAttribute in
 /home/ikosh/programs/autotools-bin/lib/libxml2.a -
 found
 
 Irina.
 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se]
 On Behalf Of Mark Abraham
 

[gmx-users] Not sure how to include dihedral angle params of ATP into force field

[Zheng Ruan]

Hi Gromacs Users,

I am trying to add ATP molecule into amber99sb-ildn force field by
using the parameters suggested in
(http://www.ncbi.nlm.nih.gov/pubmed/12759902). I known the problem has
been discussed previously, but I still cannot figure out how to
convert the torsion params proposed in the paper into gromacs.

Specifically, there is a table that describes the torsion angle
parameters in the paper:

Torsion  No._of_paths(1)  Vn/2(2)   gamma(3)  n(4)
HC-CT-OS-P   3 0.105   0.00   3.0
CT-OS-P-OS   1-1.560   0.00   1.0
CT-OS-P-O2   2 1.179   0.00  -3.0
CT-OS-P-O2   2-0.812   0.00   2.0
P-OS-P-OS1 0.897   0.00   1.0
P-CS-P-O2 2-0.709   0.00   2.0
P-CS-P-O3 3-0.255   0.00   3.0

Where
(1) Number of bond paths that the total Vn/2 is divided into.
(2) Magnitude of torsion in kcal/mol.
(3) Phase offset in degrees.
(4) The periodicity of the torsion.

I think the corresponding part in the ff is [dihedraltypes] in
ffbonded.itp, where it looks like this:
[ dihedraltypes ]
;i  j   k  l func  phase  kd  pn
CA  CA  CA  OH   4  180.00 4.60240 2; new99
H5  O   C   OH   4  180.00 4.60240 2; new99
H5  O   C   OS   4  180.00 4.60240 2; new99

I'm not quite sure about the exact physics behind these parameters.
But just by looking at the units, Vn/2 corresponds to kd; gamma
correponds to phase; and n relates to pn. What confused me is the
negative number in Vn/2 and n. What kind of unit transformation should
I do to put the params in the param table to ffbonded.itp?

Thank you!
Zheng Ruan
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Re: [gmx-users] Shrink simulation box while maintaining ensemble

[Tsjerk Wassenaar]

Hi Matthias,

There is one way that I know of, but it's a bit experimental yet. If you
want to know more, you can contact me off-list.

Best,

Tsjerk

On Mon, Feb 15, 2016 at 6:17 PM, Justin Lemkul  wrote:

>
>
> On 2/15/16 10:35 AM, Matthias Ernst wrote:
>
>> Hi,
>>
>> I am running a protein folding simulation, starting with an extended
>> structure that needs a lot of water molecules to fulfill the minimial
>> image convenction.
>> Is there a way to "shrink" a simulation box and get rid of unnecessary
>> solvent molecules while keeping velocities (to preserve the ensemble as
>> far as possible and avoid re-equilibration)?
>>
>>
> You could define a group of atoms that satisfies some geometric criterion
> (boundaries for x,y,z) with gmx select, and use trjconv with that index
> group to save only those atoms.  Assuming you're doing this on a .trr file
> with velocities, those  would be preserved.  But the complication is that
> you then have a new box (which you have to define), which puts particles at
> new positions relative to the new boundaries, and those velocities and
> positions are not necessarily compatible with this new definition (you
> could have atoms at the new boundaries that are about to crash right into
> one another!), so you probably have to re-equilibrate, anyway.
>
> -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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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] How to generate intermediates for alchemy mutation

[Mark Abraham]

Hi,

The usual way is to build a topology whose A and B states are the mutated
forms, and you then equilibrate the system separately at each lambda point
interpolating between them. You "simply" need a starting configuration with
a plausible geometry for each such point.

Mark

On Mon, Feb 15, 2016 at 9:27 PM Jagannath Mondal 
wrote:

> Dear Users
>   I want to compute the relative free energy for mutating one residue of a
> protein to another one using free energy perturbations as implemented in
> gromacs. I wanted to know how I can generate the starting configurations of
> the intermediate lambda values. Is there any interpolation scheme within
> gromacs that will let me generate the intermediate structures.
> Jagannath
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Re: [gmx-users] DSSP secondary structure

[Justin Lemkul]

On 2/15/16 3:26 PM, mohammad r wrote:

Thank you Justin,
  I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any 
way to calculate the percentage of a-helical structure of a protein during 
simulation? Indeed DSSP visualize it but I want to calculate it exactly.


It should be at the end of the scount.xvg file.

-Justin


Thanks, Mohammad.


 On Monday, February 15, 2016 6:31 PM, Justin Lemkul  
wrote:




On 2/15/16 1:31 AM, mohammad r wrote:

I changed and reduced the ratio but the xpm file was not changed at all.



Unfortunately there's not much I can tell you here because this is rather
cryptic.  It's illogical to get the same output with different input.  You can
calculate exactly what values to use based on the number of residues in the
protein (y-axis) and number of frames (x-axis).  Then scale xbox accordingly to
fit some nicely shaped rectangle of defined proportions.

-Justin



   On Sunday, February 14, 2016 5:05 PM, Justin Lemkul  
wrote:




On 2/14/16 1:54 AM, mohammad r wrote:

Thank you Justin,

I used xpm2ps command with below m2p file but the resolution was not changed.
I've attached the xpm file, even the legend can't be seen.
is there anyway to get the result file in pdf format?

m2p file (I found it in the gromacs website):




xbox = 2.0 ; x‐size of a matrix element
ybox = 2.0 ; y‐size of a matrix element


You have a rectangular matrix, with the x-dimension being much longer than the
y-dimension.  If you set these two values to be the same, what happens to the
size of the rectangle?  It gets uniformly scaled.  So naturally that
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.

-Justin





--
==

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

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

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

==
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Re: [gmx-users] DSSP secondary structure

[mohammad r]

Thank you Justin,
 I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any 
way to calculate the percentage of a-helical structure of a protein during 
simulation? Indeed DSSP visualize it but I want to calculate it exactly.
Thanks, Mohammad.
 

On Monday, February 15, 2016 6:31 PM, Justin Lemkul  wrote:
 

 

On 2/15/16 1:31 AM, mohammad r wrote:
> I changed and reduced the ratio but the xpm file was not changed at all.
>

Unfortunately there's not much I can tell you here because this is rather 
cryptic.  It's illogical to get the same output with different input.  You can 
calculate exactly what values to use based on the number of residues in the 
protein (y-axis) and number of frames (x-axis).  Then scale xbox accordingly to 
fit some nicely shaped rectangle of defined proportions.

-Justin

>
>      On Sunday, February 14, 2016 5:05 PM, Justin Lemkul  
>wrote:
>
>
>
>
> On 2/14/16 1:54 AM, mohammad r wrote:
>> Thank you Justin,
>>
>> I used xpm2ps command with below m2p file but the resolution was not changed.
>> I've attached the xpm file, even the legend can't be seen.
>> is there anyway to get the result file in pdf format?
>>
>> m2p file (I found it in the gromacs website):
>>
>
>> xbox = 2.0 ; x‐size of a matrix element
>> ybox = 2.0 ; y‐size of a matrix element
>
> You have a rectangular matrix, with the x-dimension being much longer than the
> y-dimension.  If you set these two values to be the same, what happens to the
> size of the rectangle?  It gets uniformly scaled.  So naturally that
> accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.
>
> -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] How to generate intermediates for alchemy mutation

[Jagannath Mondal]

Dear Users
  I want to compute the relative free energy for mutating one residue of a
protein to another one using free energy perturbations as implemented in
gromacs. I wanted to know how I can generate the starting configurations of
the intermediate lambda values. Is there any interpolation scheme within
gromacs that will let me generate the intermediate structures.
Jagannath
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[gmx-users] Adding chain ID with g_cluster outputs

[anu chandra]

Dear Gromcas users,

I have used g_cluster to do RMSD-based cluster analysis. Unfortunately, the
generated center structures ( with option -cl) are failed to visualize with
Pymol. I presume that one of the reason may be due to the lack of chain ID
information in the the PDB as the protein is a multimer. So I just wonder
if there is a way to incorporate chain ID while doing the g_cluster
analysis.

Any suggestion would be highly appreciated

Many thanks

Anu
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Re: [gmx-users] calculate *all* carbon atom distances over time?

[Mark Abraham]

Hi,

You can just get a cmake binary from their website and use it locally
yourself ;-)

Mark

On Mon, Feb 15, 2016 at 7:05 PM Athina Meletiou 
wrote:

> Thanks Justin :)
>
> I can't compile Gromacs 5.0 until tomorrow as I don't have sudo rights to
> update cmake to 2.8.8 :( that's why I was getting excited to know if it was
> possible with gmx distance! Will try it tomorrow hopefully. Again, thank
> you for the help.
>
> Best regards,
> Athina
>
>
>
>
> This message and any attachment are intended solely for the addressee
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Re: [gmx-users] NVT-Eq ---> NVT-MD

[Alexander Alexander]

Great explanation, thanks.
I hope you mean with "atoms have velocities" the last three columns in .gro
file you mean.

So, If I recall my first question concerning to the combining of two
sequence NVT-Eq and NVT-MD to just one longer NVT-MD after minimization
directly, then I need to turn on the velocity generation in my single
NVT-MD production.

Regards,
Alex


On Mon, Feb 15, 2016 at 6:44 PM, Justin Lemkul  wrote:

>
>
> On 2/15/16 12:40 PM, Alexander Alexander wrote:
>
>> Dear Mark,
>>
>> To be honest, I do not know exactly when and in which physics the velocity
>> generation in a MD simulation is necessary and when not !
>>
>> And I usually-historically generate velocity in the Equilibration and not
>> in Production.
>>
>> My specific case here is a pure metallic surface.
>>
>>
> Here is a simple decision structure:
>
> Do the atoms have velocities?
> If yes, don't re-generate them.
> If no, you need to generate them.
>
> gen_vel randomly assigns velocities according to a Maxwell distribution.
> If you're continuing a previous run, you already have velocities that are
> (presumably) part of the target statistical mechanical ensemble.
> Re-generating them destroys that and requires re-equilibration.  If you're
> just starting out, you've probably done an energy minimization, which has
> no velocities.  So if you try to start a simulation without generating
> velocities, your system may behave rather strangely as the thermostat tries
> to figure out how to bring the non-existent velocities into agreement with
> the target temperature.
>
> -Justin
>
>
> Regards,
>> Alex
>>
>> On Mon, Feb 15, 2016 at 6:27 PM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> Why did your two-part run need to generate velocities at a suitable
>>> temperature in the first part? Does that reason apply to your one-part
>>> run?
>>> ;-)
>>>
>>> Mark
>>>
>>> On Mon, Feb 15, 2016 at 6:23 PM Alexander Alexander <
>>> alexanderwie...@gmail.com> wrote:
>>>
>>> Thanks for your prompt response,

 Could you please confirm me that  in my single NVT-MD I should  use
 "continuation  = no" and below velocity generation, right? or velocity
 generation is not required any more?

 ;Generate velocity
 gen_vel = yes
 gen_temp = 298.15
 gen_seed = -1

 Regards,
 Alex

 On Mon, Feb 15, 2016 at 6:12 PM, Justin Lemkul  wrote:


>
> On 2/15/16 12:09 PM, Alexander Alexander wrote:
>
> Dear Gromacs user,
>>
>> I have an elementary question which I would be thankful if one could
>> comment on it;
>>
>> I want to do a NVT-MD simulation as a production calculation of my MD
>> simulation for 10 ns, and suppose that a NVT- Equilibration has been
>>
> done

> in advance for 0.5 ns. The normal differences between their .mdp files
>>
> are

> coming below and the rest of their .mdp files are fully identical;
>>
>> NVT-Eq (Equilibration)
>> 
>> nsteps  =  50; 0.5 ns
>>
>> ;Generate velocity
>> gen_vel = yes
>> gen_temp = 298.15
>> gen_seed = -1
>> -
>>
>>
>> NVT-MD (Production)
>> -
>> nsteps = 1000; 10 ns
>> continuation  = yes;continuing from NVT-Eq
>>
>>
>> ;Generate velocity
>> gen_vel = no
>> -
>>
>> Since they have identical .mdp parameters, then, my question is that:
>>
>> if it is possible to do just one NVT-MD simulation (a bit longer (10 +
>> 0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?
>>
>>
>> Of course.  The normal use for separating two phases (equilibration
> and
> production) is in the case of restraints, shorter time step for
> equilibration in troublesome systems, etc.  If you just have the same
> settings, do a single run.
>
> -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
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Re: [gmx-users] calculate *all* carbon atom distances over time?

[Athina Meletiou]

Thanks Justin :)

I can't compile Gromacs 5.0 until tomorrow as I don't have sudo rights to 
update cmake to 2.8.8 :( that's why I was getting excited to know if it was 
possible with gmx distance! Will try it tomorrow hopefully. Again, thank you 
for the help.

Best regards,
Athina




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Re: [gmx-users] calculate *all* carbon atom distances over time?

[Justin Lemkul]

On 2/15/16 12:58 PM, Athina Meletiou wrote:

Thank you for the clarification, Justin.

Does gmx distance also work in the same way? In its reference manual I see that it 
supports an -oall option ("-oall writes all the individual distances"), so 
could it be that it can print the distances between all atoms without the need of the 
extra processing (script and index file) that g_dist needs?



Try it and see :)

-Justin

--
==

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

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

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

==
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Re: [gmx-users] calculate *all* carbon atom distances over time?

[Athina Meletiou]

Thank you for the clarification, Justin.

Does gmx distance also work in the same way? In its reference manual I see that 
it supports an -oall option ("-oall writes all the individual distances"), so 
could it be that it can print the distances between all atoms without the need 
of the extra processing (script and index file) that g_dist needs?

Best regards,
Athina




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Re: [gmx-users] calculate *all* carbon atom distances over time?

[Justin Lemkul]

On 2/15/16 12:51 PM, Athina Meletiou wrote:

I apologise for the typo - I meant "create an index file in which each atom will be 
in an individual group"



Yes, at which point it is trivial to loop over all combinations of interest in a 
shell script.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] calculate *all* carbon atom distances over time?

[Athina Meletiou]

I apologise for the typo - I meant "create an index file in which each atom 
will be in an individual group"




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Re: [gmx-users] calculate *all* carbon atom distances over time?

[Athina Meletiou]

Dear Justin,

Thank you for taking the time to reply. So if I understand correctly, I can use 
g_dist for my purposes, but I have to create an index file in which each group 
will be in an individual group?

Athina




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Re: [gmx-users] NVT-Eq ---> NVT-MD

[Justin Lemkul]

On 2/15/16 12:40 PM, Alexander Alexander wrote:

Dear Mark,

To be honest, I do not know exactly when and in which physics the velocity
generation in a MD simulation is necessary and when not !

And I usually-historically generate velocity in the Equilibration and not
in Production.

My specific case here is a pure metallic surface.



Here is a simple decision structure:

Do the atoms have velocities?
If yes, don't re-generate them.
If no, you need to generate them.

gen_vel randomly assigns velocities according to a Maxwell distribution.  If 
you're continuing a previous run, you already have velocities that are 
(presumably) part of the target statistical mechanical ensemble.  Re-generating 
them destroys that and requires re-equilibration.  If you're just starting out, 
you've probably done an energy minimization, which has no velocities.  So if you 
try to start a simulation without generating velocities, your system may behave 
rather strangely as the thermostat tries to figure out how to bring the 
non-existent velocities into agreement with the target temperature.


-Justin


Regards,
Alex

On Mon, Feb 15, 2016 at 6:27 PM, Mark Abraham 
wrote:


Hi,

Why did your two-part run need to generate velocities at a suitable
temperature in the first part? Does that reason apply to your one-part run?
;-)

Mark

On Mon, Feb 15, 2016 at 6:23 PM Alexander Alexander <
alexanderwie...@gmail.com> wrote:


Thanks for your prompt response,

Could you please confirm me that  in my single NVT-MD I should  use
"continuation  = no" and below velocity generation, right? or velocity
generation is not required any more?

;Generate velocity
gen_vel = yes
gen_temp = 298.15
gen_seed = -1

Regards,
Alex

On Mon, Feb 15, 2016 at 6:12 PM, Justin Lemkul  wrote:




On 2/15/16 12:09 PM, Alexander Alexander wrote:


Dear Gromacs user,

I have an elementary question which I would be thankful if one could
comment on it;

I want to do a NVT-MD simulation as a production calculation of my MD
simulation for 10 ns, and suppose that a NVT- Equilibration has been

done

in advance for 0.5 ns. The normal differences between their .mdp files

are

coming below and the rest of their .mdp files are fully identical;

NVT-Eq (Equilibration)

nsteps  =  50; 0.5 ns

;Generate velocity
gen_vel = yes
gen_temp = 298.15
gen_seed = -1
-


NVT-MD (Production)
-
nsteps = 1000; 10 ns
continuation  = yes;continuing from NVT-Eq


;Generate velocity
gen_vel = no
-

Since they have identical .mdp parameters, then, my question is that:

if it is possible to do just one NVT-MD simulation (a bit longer (10 +
0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?



Of course.  The normal use for separating two phases (equilibration and
production) is in the case of restraints, shorter time step for
equilibration in troublesome systems, etc.  If you just have the same
settings, do a single run.

-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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==

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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

Re: [gmx-users] NVT-Eq ---> NVT-MD

[Alexander Alexander]

Dear Mark,

To be honest, I do not know exactly when and in which physics the velocity
generation in a MD simulation is necessary and when not !

And I usually-historically generate velocity in the Equilibration and not
in Production.

My specific case here is a pure metallic surface.

Regards,
Alex

On Mon, Feb 15, 2016 at 6:27 PM, Mark Abraham 
wrote:

> Hi,
>
> Why did your two-part run need to generate velocities at a suitable
> temperature in the first part? Does that reason apply to your one-part run?
> ;-)
>
> Mark
>
> On Mon, Feb 15, 2016 at 6:23 PM Alexander Alexander <
> alexanderwie...@gmail.com> wrote:
>
> > Thanks for your prompt response,
> >
> > Could you please confirm me that  in my single NVT-MD I should  use
> > "continuation  = no" and below velocity generation, right? or velocity
> > generation is not required any more?
> >
> > ;Generate velocity
> > gen_vel = yes
> > gen_temp = 298.15
> > gen_seed = -1
> >
> > Regards,
> > Alex
> >
> > On Mon, Feb 15, 2016 at 6:12 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 2/15/16 12:09 PM, Alexander Alexander wrote:
> > >
> > >> Dear Gromacs user,
> > >>
> > >> I have an elementary question which I would be thankful if one could
> > >> comment on it;
> > >>
> > >> I want to do a NVT-MD simulation as a production calculation of my MD
> > >> simulation for 10 ns, and suppose that a NVT- Equilibration has been
> > done
> > >> in advance for 0.5 ns. The normal differences between their .mdp files
> > are
> > >> coming below and the rest of their .mdp files are fully identical;
> > >>
> > >> NVT-Eq (Equilibration)
> > >> 
> > >> nsteps  =  50; 0.5 ns
> > >>
> > >> ;Generate velocity
> > >> gen_vel = yes
> > >> gen_temp = 298.15
> > >> gen_seed = -1
> > >> -
> > >>
> > >>
> > >> NVT-MD (Production)
> > >> -
> > >> nsteps = 1000; 10 ns
> > >> continuation  = yes;continuing from NVT-Eq
> > >>
> > >>
> > >> ;Generate velocity
> > >> gen_vel = no
> > >> -
> > >>
> > >> Since they have identical .mdp parameters, then, my question is that:
> > >>
> > >> if it is possible to do just one NVT-MD simulation (a bit longer (10 +
> > >> 0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?
> > >>
> > >>
> > > Of course.  The normal use for separating two phases (equilibration and
> > > production) is in the case of restraints, shorter time step for
> > > equilibration in troublesome systems, etc.  If you just have the same
> > > settings, do a single run.
> > >
> > > -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!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> >
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> > posting!
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Re: [gmx-users] NVT-Eq ---> NVT-MD

[Mark Abraham]

Hi,

Why did your two-part run need to generate velocities at a suitable
temperature in the first part? Does that reason apply to your one-part run?
;-)

Mark

On Mon, Feb 15, 2016 at 6:23 PM Alexander Alexander <
alexanderwie...@gmail.com> wrote:

> Thanks for your prompt response,
>
> Could you please confirm me that  in my single NVT-MD I should  use
> "continuation  = no" and below velocity generation, right? or velocity
> generation is not required any more?
>
> ;Generate velocity
> gen_vel = yes
> gen_temp = 298.15
> gen_seed = -1
>
> Regards,
> Alex
>
> On Mon, Feb 15, 2016 at 6:12 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 2/15/16 12:09 PM, Alexander Alexander wrote:
> >
> >> Dear Gromacs user,
> >>
> >> I have an elementary question which I would be thankful if one could
> >> comment on it;
> >>
> >> I want to do a NVT-MD simulation as a production calculation of my MD
> >> simulation for 10 ns, and suppose that a NVT- Equilibration has been
> done
> >> in advance for 0.5 ns. The normal differences between their .mdp files
> are
> >> coming below and the rest of their .mdp files are fully identical;
> >>
> >> NVT-Eq (Equilibration)
> >> 
> >> nsteps  =  50; 0.5 ns
> >>
> >> ;Generate velocity
> >> gen_vel = yes
> >> gen_temp = 298.15
> >> gen_seed = -1
> >> -
> >>
> >>
> >> NVT-MD (Production)
> >> -
> >> nsteps = 1000; 10 ns
> >> continuation  = yes;continuing from NVT-Eq
> >>
> >>
> >> ;Generate velocity
> >> gen_vel = no
> >> -
> >>
> >> Since they have identical .mdp parameters, then, my question is that:
> >>
> >> if it is possible to do just one NVT-MD simulation (a bit longer (10 +
> >> 0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?
> >>
> >>
> > Of course.  The normal use for separating two phases (equilibration and
> > production) is in the case of restraints, shorter time step for
> > equilibration in troublesome systems, etc.  If you just have the same
> > settings, do a single run.
> >
> > -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!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] NVT-Eq ---> NVT-MD

[Justin Lemkul]

On 2/15/16 12:22 PM, Alexander Alexander wrote:

Thanks for your prompt response,

Could you please confirm me that  in my single NVT-MD I should  use
"continuation  = no" and below velocity generation, right? or velocity
generation is not required any more?



Velocities should be generated at the beginning of a run (gen_vel = yes), and 
preserved (gen_vel = no) if the run is continued after being stopped.


The same applies with the "continuation" keyword.  Is it the start of a brand 
new run?  Continuation = no.  Is it a continuation of a previous run that was 
stopped?  Continuation = yes.


-Justin


;Generate velocity
gen_vel = yes
gen_temp = 298.15
gen_seed = -1

Regards,
Alex

On Mon, Feb 15, 2016 at 6:12 PM, Justin Lemkul  wrote:




On 2/15/16 12:09 PM, Alexander Alexander wrote:


Dear Gromacs user,

I have an elementary question which I would be thankful if one could
comment on it;

I want to do a NVT-MD simulation as a production calculation of my MD
simulation for 10 ns, and suppose that a NVT- Equilibration has been done
in advance for 0.5 ns. The normal differences between their .mdp files are
coming below and the rest of their .mdp files are fully identical;

NVT-Eq (Equilibration)

nsteps  =  50; 0.5 ns

;Generate velocity
gen_vel = yes
gen_temp = 298.15
gen_seed = -1
-


NVT-MD (Production)
-
nsteps = 1000; 10 ns
continuation  = yes;continuing from NVT-Eq


;Generate velocity
gen_vel = no
-

Since they have identical .mdp parameters, then, my question is that:

if it is possible to do just one NVT-MD simulation (a bit longer (10 +
0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?



Of course.  The normal use for separating two phases (equilibration and
production) is in the case of restraints, shorter time step for
equilibration in troublesome systems, etc.  If you just have the same
settings, do a single run.

-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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--
==

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] RMSD reproducibility

[Justin Lemkul]

On 2/15/16 12:21 PM, Biplab Ghosh wrote:

Dear Gromacs Users,

I have the following question:

Suppose I repeat a simulation, keeping everything exactly the same.
What will happen to RMSD? Will it be exactly same with the previous run?


No.


If not, then how much variation is expected?



Impossible to tell.  RMSD is also a useless metric in this regard.


To check this, I ran two independent simulations:
1) upto t=100ns using 216 processors and
2) upto t=200ns using 432 processors.
Everything else were kept unchanged!

The calculated RMSD for upto t=100ns was quite different.
Am I doing something  wrong? Please explain.



Welcome to the chaotic world of MD.  Deviations occur very rapidly due to a 
number of factors.  This is why it is commonplace to run multiple simulations to 
confirm results.  One trajectory alone is usually insufficient evidence that the 
findings are conclusive.


http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

--
==

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

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

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

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Re: [gmx-users] NVT-Eq ---> NVT-MD

[Alexander Alexander]

Thanks for your prompt response,

Could you please confirm me that  in my single NVT-MD I should  use
"continuation  = no" and below velocity generation, right? or velocity
generation is not required any more?

;Generate velocity
gen_vel = yes
gen_temp = 298.15
gen_seed = -1

Regards,
Alex

On Mon, Feb 15, 2016 at 6:12 PM, Justin Lemkul  wrote:

>
>
> On 2/15/16 12:09 PM, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> I have an elementary question which I would be thankful if one could
>> comment on it;
>>
>> I want to do a NVT-MD simulation as a production calculation of my MD
>> simulation for 10 ns, and suppose that a NVT- Equilibration has been done
>> in advance for 0.5 ns. The normal differences between their .mdp files are
>> coming below and the rest of their .mdp files are fully identical;
>>
>> NVT-Eq (Equilibration)
>> 
>> nsteps  =  50; 0.5 ns
>>
>> ;Generate velocity
>> gen_vel = yes
>> gen_temp = 298.15
>> gen_seed = -1
>> -
>>
>>
>> NVT-MD (Production)
>> -
>> nsteps = 1000; 10 ns
>> continuation  = yes;continuing from NVT-Eq
>>
>>
>> ;Generate velocity
>> gen_vel = no
>> -
>>
>> Since they have identical .mdp parameters, then, my question is that:
>>
>> if it is possible to do just one NVT-MD simulation (a bit longer (10 +
>> 0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?
>>
>>
> Of course.  The normal use for separating two phases (equilibration and
> production) is in the case of restraints, shorter time step for
> equilibration in troublesome systems, etc.  If you just have the same
> settings, do a single run.
>
> -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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> posting!
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>
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[gmx-users] RMSD reproducibility

[Biplab Ghosh]

Dear Gromacs Users,

I have the following question:

Suppose I repeat a simulation, keeping everything exactly the same.
What will happen to RMSD? Will it be exactly same with the previous run?
If not, then how much variation is expected?

To check this, I ran two independent simulations:
1) upto t=100ns using 216 processors and
2) upto t=200ns using 432 processors.
Everything else were kept unchanged!

The calculated RMSD for upto t=100ns was quite different.
Am I doing something  wrong? Please explain.

Regards
Biplab.






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Re: [gmx-users] Shrink simulation box while maintaining ensemble

[Justin Lemkul]

On 2/15/16 10:35 AM, Matthias Ernst wrote:

Hi,

I am running a protein folding simulation, starting with an extended
structure that needs a lot of water molecules to fulfill the minimial
image convenction.
Is there a way to "shrink" a simulation box and get rid of unnecessary
solvent molecules while keeping velocities (to preserve the ensemble as
far as possible and avoid re-equilibration)?



You could define a group of atoms that satisfies some geometric criterion 
(boundaries for x,y,z) with gmx select, and use trjconv with that index group to 
save only those atoms.  Assuming you're doing this on a .trr file with 
velocities, those  would be preserved.  But the complication is that you then 
have a new box (which you have to define), which puts particles at new positions 
relative to the new boundaries, and those velocities and positions are not 
necessarily compatible with this new definition (you could have atoms at the new 
boundaries that are about to crash right into one another!), so you probably 
have to re-equilibrate, anyway.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] calculate *all* carbon atom distances over time?

[Justin Lemkul]

On 2/15/16 12:10 PM, Athina Meletiou wrote:

Hello all,

I was wondering how I could measure the distance over time between all my
carbon atoms in my simulation. My molecules have interesting folding patterns
and I would like to see the distances between the unconnected carbon atoms as
my molecules fold and unfold through the simulation. My simulations consist
of single lipid molecules in water.

I have tried using g_dist but it seems that it's not what I'm looking for as
it calculates distances between groups of atoms rather than individual atoms.


A "group" can be one atom.


Do you think that gmx distance (Gromacs 5.0) will help me? What concerns me
is that in the gmx distance reference it states that "gmx distance calculates
distances between pairs of positions as a function of time" - do the
positions need to be in pairs, as in always in even numbers?



If you're looking at distances between any two atoms, why would this be a 
concern?

-Justin

--
==

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

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

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

==
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Re: [gmx-users] NVT-Eq ---> NVT-MD

[Justin Lemkul]

On 2/15/16 12:09 PM, Alexander Alexander wrote:

Dear Gromacs user,

I have an elementary question which I would be thankful if one could
comment on it;

I want to do a NVT-MD simulation as a production calculation of my MD
simulation for 10 ns, and suppose that a NVT- Equilibration has been done
in advance for 0.5 ns. The normal differences between their .mdp files are
coming below and the rest of their .mdp files are fully identical;

NVT-Eq (Equilibration)

nsteps  =  50; 0.5 ns

;Generate velocity
gen_vel = yes
gen_temp = 298.15
gen_seed = -1
-


NVT-MD (Production)
-
nsteps = 1000; 10 ns
continuation  = yes;continuing from NVT-Eq


;Generate velocity
gen_vel = no
-

Since they have identical .mdp parameters, then, my question is that:

if it is possible to do just one NVT-MD simulation (a bit longer (10 +
0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?



Of course.  The normal use for separating two phases (equilibration and 
production) is in the case of restraints, shorter time step for equilibration in 
troublesome systems, etc.  If you just have the same settings, do a single run.


-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] calculate *all* carbon atom distances over time?

[Athina Meletiou]

Hello all,

I was wondering how I could measure the distance over time between all my 
carbon atoms in my simulation. My molecules have interesting folding patterns 
and I would like to see the distances between the unconnected carbon atoms as 
my molecules fold and unfold through the simulation. My simulations consist of 
single lipid molecules in water.

I have tried using g_dist but it seems that it's not what I'm looking for as it 
calculates distances between groups of atoms rather than individual atoms. Do 
you think that gmx distance (Gromacs 5.0) will help me? What concerns me is 
that in the gmx distance reference it states that "gmx distance calculates 
distances between pairs of positions as a function of time" - do the positions 
need to be in pairs, as in always in even numbers?

Thank you all very much,

Athina




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[gmx-users] NVT-Eq ---> NVT-MD

[Alexander Alexander]

Dear Gromacs user,

I have an elementary question which I would be thankful if one could
comment on it;

I want to do a NVT-MD simulation as a production calculation of my MD
simulation for 10 ns, and suppose that a NVT- Equilibration has been done
in advance for 0.5 ns. The normal differences between their .mdp files are
coming below and the rest of their .mdp files are fully identical;

NVT-Eq (Equilibration)

nsteps  =  50; 0.5 ns

;Generate velocity
gen_vel = yes
gen_temp = 298.15
gen_seed = -1
-


NVT-MD (Production)
-
nsteps = 1000; 10 ns
continuation  = yes;continuing from NVT-Eq


;Generate velocity
gen_vel = no
-

Since they have identical .mdp parameters, then, my question is that:

if it is possible to do just one NVT-MD simulation (a bit longer (10 +
0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?

Best regards,
Alex
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Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Irina Kosheleva]

Hi Mark,
Thank you for your suggestions
Indeed this works:
For libxml2:
./configure --prefix=/home/ikosh/programs/autotools-bin  --without-python 
--without-zlib --without-lzma

cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r 
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX 
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  
-DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" 
-DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
-- Looking for NVIDIA GPUs present in the system

-- Checking for MPI_IN_PLACE - yes
-- Looking for zlibVersion in /home/ikosh/programs/autotools-bin/lib/libz.a
-- Looking for zlibVersion in /home/ikosh/programs/autotools-bin/lib/libz.a - 
found
-- Found LibXml2: /home/ikosh/programs/autotools-bin/lib/libxml2.a (found 
version "2.9.3") 
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a - 
found

Irina.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Monday, February 15, 2016 9:30 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi,

Now that I have a computer again, I looked up what I did on Vesta, and in
fact you don't need zlib support from libxml2, so just configure libxml2
without that (and without python), and you'll be fine.

I am also looking at how we can take this useless activity away from
people...

Mark
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[gmx-users] Shrink simulation box while maintaining ensemble

[Matthias Ernst]

Hi,

I am running a protein folding simulation, starting with an extended
structure that needs a lot of water molecules to fulfill the minimial
image convenction.
Is there a way to "shrink" a simulation box and get rid of unnecessary
solvent molecules while keeping velocities (to preserve the ensemble as
far as possible and avoid re-equilibration)?

Thanks,
Matthias

-- 
Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611
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Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Mark Abraham]

Hi,

Now that I have a computer again, I looked up what I did on Vesta, and in
fact you don't need zlib support from libxml2, so just configure libxml2
without that (and without python), and you'll be fine.

I am also looking at how we can take this useless activity away from
people...

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

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Irina Kosheleva]

Hi Mark,
I implemented your suggestions.
It looks like gromacs can find zlib (through CMAKE_PREFIX_PATH I presume) but 
have errors in libxml2.a , which are related to zlib functions.
Please see below.
Irina.

I have configure $PATH, LD_LIBRARY_PATH and CMAKE_PREFIX_PATH to point to my 
directories also:
echo $PATH
/home/ikosh/programs/autotools-bin/bin:
echo $LD_LIBRARY_PATH 
/home/ikosh/programs/autotools-bin/lib:

echo $CMAKE_PREFIX_PATH
/home/ikosh/programs/autotools-bin:

For libxml2-2.9.3 in my dir:
./configure --prefix=/home/ikosh/programs/autotools-bin  
--with-python-install-dir=/home/ikosh/programs/autotools-bin 
Otherwise it tries to install  python in top directories
It found zlib just OK:
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
Checking zlib
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzread in -lz... yes


NOW for gromacs compilation:

cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r 
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX 
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  
-DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" 
-DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install

---
-- Checking for MPI_IN_PLACE - yes
-- Looking for zlibVersion in /home/ikosh/programs/autotools-bin/lib/libz.a
-- Looking for zlibVersion in /home/ikosh/programs/autotools-bin/lib/libz.a - 
found
-- Found LibXml2: /home/ikosh/programs/autotools-bin/lib/libxml2.a (found 
version "2.9.3") 
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
-- Looking for include file pthread.h
--

TAIL CMakeFiles/CMakeError.log
Determining if the function xmlTextWriterEndAttribute exists in the 
/home/ikosh/programs/autotools-bin/lib/libxml2.a failed with the following 
output:
Change Dir: /home/ikosh/gromacs-5.1.1/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_9d85a/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_9d85a.dir/build.make 
CMakeFiles/cmTC_9d85a.dir/build
gmake[1]: Entering directory 
`/gpfs/vesta-home/ikosh/gromacs-5.1.1/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_9d85a.dir/CheckFunctionExists.c.o
/soft/compilers/wrappers/xl/mpixlc_r  
-I/bgsys/drivers/ppcfloor/comm/sys/include -I/bgsys/drivers/ppcfloor/ 
-I/bgsys/drivers/ppcfloor/spi/include 
-I/bgsys/drivers/ppcfloor/spi/include/kernel/cnk 
-I/bgsys/drivers/ppcfloor/comm/xl/include -O3 -qsmp=omp -qarch=qp -qtune=qp 
-qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-030 -qlanglvl=extc99 
-qarch=auto -qtune=auto  -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute   -o 
CMakeFiles/cmTC_9d85a.dir/CheckFunctionExists.c.o -c 
/soft/buildtools/cmake/3.3.0/share/cmake-3.3/Modules/CheckFunctionExists.c
Linking C executable cmTC_9d85a
/soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_9d85a.dir/link.txt --verbose=1
/soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp 
-qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-030 
-qlanglvl=extc99 -qarch=auto -qtune=auto  
-DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
CMakeFiles/cmTC_9d85a.dir/CheckFunctionExists.c.o  -o cmTC_9d85a  
/home/ikosh/programs/autotools-bin/lib/libxml2.a 
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpenW':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to `gzopen'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to 
`gzdopen'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`__xmlParserInputBufferCreateFilename':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to 
`gzdirect'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlFreeZMemBuff':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to 
`deflateEnd'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpen_real':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1167: undefined reference to 
`gzdopen'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1198: undefined reference to `gzopen'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileClose':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1331: undefined reference to 
`gzclose'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileWrite':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1315: undefined reference to 
`gzwrite'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlZMemBuffGetContent':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1758: undefined reference to 
`deflate'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlZMemBuffAppend':

Re: [gmx-users] Porting to Gromacs of Parmbsc1

[Mark Abraham]

Hi,

Not to my knowledge, but at the page you linked, BSC recommends using
AmberTools and ACPYPE...

Mark

On Mon, 15 Feb 2016 15:18 Sarath Chandra 
wrote:

> A forcefield on Parmbsc1 is out and it has reportedly fixed some issues
> with DNA structures
>
> http://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html
> http://mmb.irbbarcelona.org/ParmBSC1/help.php?id=download
>
> Is there a script to convert lib and frcmod files to a newFF.ff directory
> and then check the forcefield for validation?
>
> Regards,
>
> Sarath
>
>
>
>
>
> Validating would be running some test systems
>
> On 14 February 2016 at 20:24, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Nobody's working on it to my knowledge, but if a forcefield has been
> > published, seems likely to be of use to multiple people, and a validation
> > script can show it works correctly with respect to the reference
> > implementation, then we'll consider it for inclusion in GROMACS.
> >
> > Mark
> >
> > On Sun, 14 Feb 2016 14:39 Sarath Chandra 
> > wrote:
> >
> > > I wish to use Parmbsc1 for DNA simulations. Are there any timelines to
> > port
> > > Parmbsc1 into Gromacs along with amber14sb?
> > >
> > > Regards,
> > >
> > > Sarath
> > > --
> > > 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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> > >
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Re: [gmx-users] DSSP secondary structure

[Justin Lemkul]

On 2/15/16 1:31 AM, mohammad r wrote:

I changed and reduced the ratio but the xpm file was not changed at all.



Unfortunately there's not much I can tell you here because this is rather 
cryptic.  It's illogical to get the same output with different input.  You can 
calculate exactly what values to use based on the number of residues in the 
protein (y-axis) and number of frames (x-axis).  Then scale xbox accordingly to 
fit some nicely shaped rectangle of defined proportions.


-Justin



 On Sunday, February 14, 2016 5:05 PM, Justin Lemkul  
wrote:




On 2/14/16 1:54 AM, mohammad r wrote:

Thank you Justin,

I used xpm2ps command with below m2p file but the resolution was not changed.
I've attached the xpm file, even the legend can't be seen.
is there anyway to get the result file in pdf format?

m2p file (I found it in the gromacs website):




xbox = 2.0 ; x‐size of a matrix element
ybox = 2.0 ; y‐size of a matrix element


You have a rectangular matrix, with the x-dimension being much longer than the
y-dimension.  If you set these two values to be the same, what happens to the
size of the rectangle?  It gets uniformly scaled.  So naturally that
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.

-Justin



--
==

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

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

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

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Re: [gmx-users] How I merge all .tpr files

[Justin Lemkul]

On 2/15/16 1:28 AM, Abid Channa wrote:

Dear Gromacs users,
I have run 50 ns simulation job in five steps. Now I am going to analyze  
energy, rmsd, rmsf etc of these simulations. I have merged all files like .gro, 
.xtc, .edr etc. But I want to merge all extend tpr files in one file for 
analyzing purpose. Is there any command to merge all .tpr files in single file. 
or any other way to analyze these tpr files kindly give your suggestions.


Merging .tpr files makes no sense and as such there is no way to do it.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] genebox and solvate command

[Justin Lemkul]

On 2/15/16 2:07 AM, Mehreen Jan wrote:

  when I have run the genbox command, it has shown that "This tool has been 
removed from Gromacs
5.0. Please see
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
for ideas how to perform the same tasks with the new tools."


In gromacs site, it is written that
genbox

This tool has been split to gmx solvate and gmx insert-molecules.
gmx

for solvate command:
solvate -cp *.pdb -cs spc216.gro -p topol.top -o *.pdb

  error:
undefined solute box
create one with gmx editconf or give expicit -box command line option??


what about gene box???


with "gmx help solvate"  and "gmx help
insert-molecules it is not clear what should i do???
what command are used???



The error message tells you exactly what to do:

"create one with gmx editconf or give expicit -box command line option"

You're trying to solvate a system that does not have a defined size, so clearly 
that fails.  Do some basic tutorials and you will see what to do.  "gmx solvate" 
is basically identical to "genbox" in this regard.  Since 5.0, the only thing 
that has changed is that the ability to insert molecules into the box has been 
split off into a separate tool.  Otherwise "gmx solvate" and "genbox" are 
actually identical for all practical purposes.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] Porting to Gromacs of Parmbsc1

[Sarath Chandra]

A forcefield on Parmbsc1 is out and it has reportedly fixed some issues
with DNA structures

http://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html
http://mmb.irbbarcelona.org/ParmBSC1/help.php?id=download

Is there a script to convert lib and frcmod files to a newFF.ff directory
and then check the forcefield for validation?

Regards,

Sarath





Validating would be running some test systems

On 14 February 2016 at 20:24, Mark Abraham  wrote:

> Hi,
>
> Nobody's working on it to my knowledge, but if a forcefield has been
> published, seems likely to be of use to multiple people, and a validation
> script can show it works correctly with respect to the reference
> implementation, then we'll consider it for inclusion in GROMACS.
>
> Mark
>
> On Sun, 14 Feb 2016 14:39 Sarath Chandra 
> wrote:
>
> > I wish to use Parmbsc1 for DNA simulations. Are there any timelines to
> port
> > Parmbsc1 into Gromacs along with amber14sb?
> >
> > Regards,
> >
> > Sarath
> > --
> > 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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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] PM3-AD ERROR GROMACS 5.1.1

[Mark Abraham]

Hi,

Yes, fixed in 5.1.2. See
http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#removed-mdrun-fatal-error-with-p3m-ad

Mark

On Mon, Feb 15, 2016 at 1:46 PM Tuanan Lourenço 
wrote:

> Hi to all,
>
> I am trying to perform a simulation utilizing the PM3-AD method but I
> received this message of error:
>
> Fatal error: Unsupported electrostatic interaction: P3M-AD
>
> Can Anybody confirm to me, if this message is due to a bug in the GROMACS
> 5.1.1?
> __
> MSc. Tuanan C Lourenço
> Ph.D Student Physical Chemistry - Universidade Federal Fluminense
> Molecular Modelling and Computer Simullation Group - UFF
> MOLMOD-CS WEBSITE 
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Re: [gmx-users] correct rlist and Verlet scheme

[Mark Abraham]

Hi,

On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev 
wrote:

> I've studied the relevant sections of the manual, but I don't consider
> myself to be familiar enough with this field to successfully guess the
> right settings.
>
> ff99sb-ildn is included in the gromacs distribution, so shouldn’t be
> there some recommended settings for it?


Ideally, yes. But nobody has made a particular effort for that combination.

Or else how was it tested to run
> properly?
>

In principle, one would have to e.g. show that
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/ can be replicated.
That's not a straightforward proposition...


> For now I've settled on the following parameters (the following is
> copied from mdout.mdp):
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; cut-off scheme (Verlet: particle based cut-offs, group: using charge
> groups)
> cutoff-scheme= Verlet
> ; nblist update frequency
> nstlist  = 40
> ; ns algorithm (simple or grid)
> ns_type  = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc  = xyz
> periodic-molecules   = no
> ; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
> ; a value of -1 means: use rlist
> verlet-buffer-tolerance  = 0.005
> ; nblist cut-off
> rlist= 1.0
> ; long-range cut-off for switched potentials
> rlistlong= 1.05
> nstcalclr= -1
>

You've no doubt read
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html and
the comments above and realize that your choices for rlist and rlistlong
are ignored with the Verlet scheme. If you want to exactly follow the
paper, you need to set verlet-buffer-tolerance=-1, nstlist to whatever
implements 10fs given your choice of time step, and rlist to 1.05. This
will run rather slower than the Verlet-scheme defaults, particularly on
GPUs, for no known advantage. You can observe the difference in speed
yourself, of course. Your call.

Mark

; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = PME
> coulomb-modifier = Potential-shift-Verlet
> rcoulomb-switch  = 0
> rcoulomb = 1.0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon-r= 1
> epsilon-rf   = 0
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> vdw-modifier = Potential-shift-Verlet
> ; cut-off lengths
> rvdw-switch  = 0
> rvdw = 1.0
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Separate tables between energy group pairs
> energygrp-table  =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.16
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier-nx   = 0
> fourier-ny   = 0
> fourier-nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald-rtol   = 1e-05
> ewald-rtol-lj= 0.001
> lj-pme-comb-rule = Geometric
> ewald-geometry   = 3d
> epsilon-surface  = 0
>
> And this is what the paper on it says:
>
> Each system was equilibrated at 300 K and 1 atm with 2.4 ns of MD
> simulation in the NPT ensemble. Then, MD simulations were carried
> out in the NVT ensemble for 720 ns using the Nosé-Hoover thermostat
> with a relaxation time of 1 ps. All simulations were performed using
> the Desmond MD program^16
>  version
> 2.1.1.0 and either the Amber ff99SB^7
>  or the
> modified Amber ff99SB force field described herein, which we have
> termed ff99SB-ILDN. All bonds involving hydrogen atoms were
> constrained with the SHAKE algorithm.^17
>  A cutoff
> of 10 Å was used for the Lennard-Jones interaction and the
> short-range electrostatic interactions. The smooth particle mesh
> Ewald method^18
>  with a
> 32 × 32 × 32 grid and a fourth-order interpolation scheme was used
> to compute the long-range electrostatic interactions. The pairlists
> were updated every 10 fs with a cutoff of 10.5 Å. We used a
> multistep RESPA scheme^19
>  for the
> integration of the equations of motion with timesteps of 2.0, 2.0,
> and 6.0 fs for the bonded, short-range nonbonded, and long-range
> nonbonded interactions, respectively. To check for potential biases
> introduced by long-range interactions between peptides in periodic
> 

[gmx-users] Order parameter

[sujithkakkat .]

Dear all,

 I am using GROMACS-4.6.5 for studying gas hydrates and related
systems.
A useful order parameter which indicates water to hydrate transition is the
F4 order parameter where F4 is related to the H--O--O--H dihedral angle for
a pair of water molecules.

   It is found that F4 parameter is very frequently mentioned in several
works on gas hydrates done using GROMACS.  I want to know whether GROMACS
can calculate the value of the F4 parameter. Or is it possible for the user
to define an order parameter?

The g_hydorder tool in GROMACS refers to an order parameter different in
definition from the F4 parameter.  (P.-L. Chau and A.J. Hardwick, Mol.
Phys., 93, (1998), 511-518.)

Please comment.

Regards,
Sujith.
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[gmx-users] PM3-AD ERROR GROMACS 5.1.1

[Tuanan Lourenço]

Hi to all,

I am trying to perform a simulation utilizing the PM3-AD method but I
received this message of error:

Fatal error: Unsupported electrostatic interaction: P3M-AD

Can Anybody confirm to me, if this message is due to a bug in the GROMACS
5.1.1?
__
MSc. Tuanan C Lourenço
Ph.D Student Physical Chemistry - Universidade Federal Fluminense
Molecular Modelling and Computer Simullation Group - UFF
MOLMOD-CS WEBSITE 
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Re: [gmx-users] which source file is handling for writing distance restraint potential energy to edr file?

[Yuno Lee]

Thank you for suggestions, Mark

I solved this problem with simply changing the one line (448) in
/src/gmxlib/disre.c file (gromacs ver 4.5.4)
fromvtot += 0.5*k0*sqr(tav_viol);
tovtot += -k0*tav_viol;

and reinstall the gromacs.

ta_disres() returns vtot variable and ifunc.c write the variable to edr file

I checked with g_energy result whether Dis. Rest. value is correct or not.

The testing result was good enough.

--

Hi,

There isn't a single place that handles this, and you don't want to get
involved ;-) What you can do is get the forces via
ahttp://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
using .tpr
files that do and do not have the restraints, read the two sets of forces
into some program you write, and subtract the results.

Mark


2016-02-15 16:44 GMT+09:00 Yuno Lee :

> Dear Gromacs users,
>
> Is there someone that can help me to find out
> which source file handles writing distance restraint potential energy to
> edr file?
>
> I want to extract the restrained force instead of potential energy through
> changing the source code.
>
>
> Any help would be appreciated.
>
> --
> Thanks & Regards,
>
>
> Yuno Lee, Ph.D.
> ---
>
> Theoretical and Computational Biophysics Lab (Prof. Changbong Hyeon)
> School of Computational Sciences, Korea Institute for Advanced Study
> (KIAS)
> 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Korea
> Tel: 82-2-958-3889, Mobile : 82-10-9396-2729
> Fax: 82-2-958-3820
> E-mail : yunol...@kias.re.kr; *yunol...@gmail.com *
>



-- 
Thanks & Regards,


Yuno Lee, Ph.D.
---

*KIAS www.kias.re.kr *
*Lee, Yuno*
Research Fellow
Theoretical and Computational Biophysics Lab (Prof. Changbong Hyeon)
School of Computational Sciences, Korea Institute for Advanced Study (KIAS)
85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Korea
Tel: 82-2-958-3889, Mobile : 82-10-9396-2729
Fax: 82-2-958-3820
E-mail : yunol...@kias.re.kr; *yunol...@gmail.com *
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Re: [gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

I've studied the relevant sections of the manual, but I don't consider 
myself to be familiar enough with this field to successfully guess the 
right settings.


ff99sb-ildn is included in the gromacs distribution, so shouldn’t be 
there some recommended settings for it? Or else how was it tested to run 
properly?


For now I've settled on the following parameters (the following is 
copied from mdout.mdp):


; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs, group: using charge 
groups)

cutoff-scheme= Verlet
; nblist update frequency
nstlist  = 40
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic-molecules   = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance  = 0.005
; nblist cut-off
rlist= 1.0
; long-range cut-off for switched potentials
rlistlong= 1.05
nstcalclr= -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch  = 0
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 1
epsilon-rf   = 0
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Separate tables between energy group pairs
energygrp-table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.16
; FFT grid size, when a value is 0 fourierspacing will be used
fourier-nx   = 0
fourier-ny   = 0
fourier-nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald-rtol   = 1e-05
ewald-rtol-lj= 0.001
lj-pme-comb-rule = Geometric
ewald-geometry   = 3d
epsilon-surface  = 0

And this is what the paper on it says:

   Each system was equilibrated at 300 K and 1 atm with 2.4 ns of MD
   simulation in the NPT ensemble. Then, MD simulations were carried
   out in the NVT ensemble for 720 ns using the Nosé-Hoover thermostat
   with a relaxation time of 1 ps. All simulations were performed using
   the Desmond MD program^16
    version
   2.1.1.0 and either the Amber ff99SB^7
    or the
   modified Amber ff99SB force field described herein, which we have
   termed ff99SB-ILDN. All bonds involving hydrogen atoms were
   constrained with the SHAKE algorithm.^17
    A cutoff
   of 10 Å was used for the Lennard-Jones interaction and the
   short-range electrostatic interactions. The smooth particle mesh
   Ewald method^18
    with a
   32 × 32 × 32 grid and a fourth-order interpolation scheme was used
   to compute the long-range electrostatic interactions. The pairlists
   were updated every 10 fs with a cutoff of 10.5 Å. We used a
   multistep RESPA scheme^19
    for the
   integration of the equations of motion with timesteps of 2.0, 2.0,
   and 6.0 fs for the bonded, short-range nonbonded, and long-range
   nonbonded interactions, respectively. To check for potential biases
   introduced by long-range interactions between peptides in periodic
   images, we repeated these simulations for four of the amino acids
   (Xaa: Ile, Leu, Asp, and Asn) using a larger box with side length 37
   Å. We found that the results of these control simulations were
   within error of those using the smaller box sizes.


12.02.2016 22:06, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 1
Date: Fri, 12 Feb 2016 14:09:28 +
From: Mark Abraham
To:"gromacs.org_gmx-users@maillist.sys.kth.se"
,  
"gmx-us...@gromacs.org"

Subject: Re: [gmx-users] correct rlist and Verlet scheme
Message-ID:

Content-Type: text/plain; charset=UTF-8

Hi,

As Adam says, you want to understand the reason why the forcefield
specifies the settings it does. For example, until at least AMBER 2003,
their force field papers did not specify PME parameters more precisely than
"x nm cutoff was used." If PME was used at all.;-)  So you can be guided
also by the parameters 

[gmx-users] the helical axis of a triple helix

[Ming Tang]

Dear list,

I want to calculate the trajectory of the helical axis of a triple helix. Do 
you have any suggestions for me to achieve this?
Any suggestions is appreciated.

Thanks,
Ming

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