[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 12

Thu May 5 04:36:38 CEST 2016

thanks Justin Lemkul.
i am using all units in Angstrom and kj/mole. soif the default of disre-fc is 1000 kj mol-1 nm-2 , what it would be in kj mol-1 A-2. i am trying to convert it through google but the number isn't looking satisfying. i know 1nm =10 A.
 Sana Saeed Khan,
Research Assistant
Chemoinformatics Lab
Graduate Student, MS bioinfo
Department of Bioinformatics
Soongsil University, Seoul, South Korea.

On Thursday, May 5, 2016 11:31 AM, Sana Saeed <bioinformatic.lady at yahoo.com> wrote:

Sana Saeed Khan,
Research Assistant
Chemoinformatics Lab
Graduate Student, MS bioinfo
Department of Bioinformatics
Soongsil University, Seoul, South Korea.

On Wednesday, May 4, 2016 9:33 PM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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Today's Topics:

   1. Re: restraints definition in mdp (Justin Lemkul)
   2. persistent jumps in trajectories (morpheus)
   3. Re: restraints definition in mdp (Justin Lemkul)
   4. Re: persistent jumps in trajectories (Justin Lemkul)
   5. restarts (ingram)

----------------------------------------------------------------------

Message: 1
Date: Wed, 4 May 2016 06:04:01 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org, Sana Saeed <bioinformatic.lady at yahoo.com>
Subject: Re: [gmx-users] restraints definition in mdp
Message-ID: <c3f00e72-8d83-909b-1f88-c9302e9730b7 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 5/4/16 4:08 AM, Sana Saeed wrote:
> hi gromacs experts
> i have applied distance, angle and dihedral restraints to my ligand in a protein's pocket so that it doesnt roam around when i turn off all interactions during simulation. do i need to mention about these restraints in the mdp file? i am using gromacs 5.0 and 5.1. i have used intermolecular_interactions directive for defining these restraints.

There is nothing in the .mdp file related to these.

> MY SECOND QUESTION is that the force constant i used is 41.840 kj/mol/K for angle and dihedral restr. does that mean that the Force constant for distance restraint is also 41.840? as i am calculating free energy of restraints (part of absolute binding F.E) so i need force constant for distance also.
>

The force constant can be whatever you want it to be.

-Justin

> [ intermolecular-interactions ]
> [ distance_restraints ]
> ;   i     j type label      funct         lo        up1        up2     weight
>   768  2131 1     0          1   0.640512   0.840512    1.84051          1
>
> [ angle_restraints ]
> ;   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB    multB
>    770   768    2131  768  1      43.420    0.0   1      43.420   41.840    1
>    768   2131   2125  2131 1     114.89    0.0   1      114.89   41.840    1
>
> [ dihedral_restraints ]
> ;   ai    aj    ak    al  type    phiA     dphiA  fcA    phiB      dphiB  fcB
>   782  770   768   2131  1       -152.840  0.0  0.0    -152.840    0.0  41.840
>   770  768   2131  2125  1       -46.638  0.0  0.0     -46.638     0.0  41.840
>   768  2131  2125  2132  1       -42.465   0.0  0.0    -42.465     0.0  41.840
>
>
> Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>

-- 
==================================================

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

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

==================================================

------------------------------

Message: 2
Date: Wed, 4 May 2016 11:12:38 +0100
From: morpheus <morpheus.sommer2008 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] persistent jumps in trajectories
Message-ID:
    <CAFzMmMYg6eA=kg_cMa9QX5BDBhojACkUzYLTiEW-gb4q4OLxbg at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi,

I'm having problems getting jumps out of my trajectories. Usually I follow
the suggestion of the Gromacs website (
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions)
and convert my trajectories with the perl script below: remove water, make
it whole, cluster, nojump, center and fit.

For previous projects these steps always did the job right.

But unfortunately this does not work for long simulations (1500 ns) of
PDB-ID 2RVD (a peptide of only 10 amino acids). I have performed the
simulation multiple times and after about 300-500 ns the jumps  still start
even after processing the trajectories as given below. With jumps I mean
this: http://s32.postimg.org/z8p90wf51/jump.jpg

Doing analysis on the trajectories with e.g. g_dist yields ?There were 4
inconsistent shifts. Check your topology?.

I am wondering what I am doing wrong and how can I fix the trajectories?

Here is the script that I am usually using:

my $bn = $ARGV[0]; # base name

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f ".$bn.".md.xtc -s
".$bn.".md.tpr -o ".$bn.".noWater.md.xtc -skip 10 << Ende \n1\n1\n << Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f ".$bn.".noWater.md.xtc
-s ".$bn.".md.tpr -o ".$bn.".noWater.whole.md.xtc -pbc whole << Ende
\n1\n1\n << Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
".$bn.".noWater.whole.md.xtc -s ".$bn.".md.tpr -o
".$bn.".noWater.whole.cluster.md.xtc -pbc cluster << Ende \n1\n1\n << Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
".$bn.".noWater.whole.cluster.md.xtc -s ".$bn.".md.tpr -o
".$bn.".noWater.whole.cluster.nojump.md.xtc -pbc nojump << Ende \n1\n1\n <<
Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
".$bn.".noWater.whole.cluster.nojump.md.xtc -s ".$bn.".md.tpr -o
".$bn.".noWater.whole.cluster.nojump.center.md.xtc -center << Ende \n1\n1\n
<< Ende";

system $cmd;

$cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
".$bn.".noWater.whole.cluster.nojump.center.md.xtc -s ".$bn.".md.tpr -o
".$bn.".final.md.xtc -fit rot+trans << Ende \n1\n1\n << Ende";

system $cmd;

Can anyone help?

Thanks!

Morpheus

------------------------------

Message: 3
Date: Wed, 4 May 2016 06:14:55 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] restraints definition in mdp
Message-ID: <fbd1f9fa-241e-7ad4-98c4-889a929ba05f at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

On 5/4/16 6:12 AM, Sana Saeed wrote:
> but i didnt specified force constant for distance ..is that fine? see my topology file contents following:
>

Sorry; misread "distance" as "dihedral." Yes, there are .mdp options for 
distance restraints.

http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#nmr-refinement

The weighting factor is multiplied by disre-fc, which defaults to 1000.

-Justin

> [ intermolecular-interactions ]
> [ distance_restraints ]
> ;  i    j type label      funct        lo        up1        up2    weight
> 768  2131 1    0          1  0.640512  0.840512    1.84051          1
>
> [ angle_restraints ]
> ;  ai    aj    ak    al  type    thA      fcA    multA  thB      fcB    multB
> 770  768    2131  768  1      43.420    0.0  1      43.420  41.840    1
> 768  2131  2125  2131 1    114.89    0.0  1      114.89  41.840    1
>
> [ dihedral_restraints ]
> ;  ai    aj    ak    al  type    phiA    dphiA  fcA    phiB      dphiB  fcB
> 782  770  768  2131  1      -152.840  0.0  0.0    -152.840    0.0  41.840
> 770  768  2131  2125  1      -46.638  0.0  0.0    -46.638    0.0  41.840
> 768  2131  2125  2132  1      -42.465  0.0  0.0    -42.465    0.0  41.840
>
>
>  Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
>
> On Wednesday, May 4, 2016 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/4/16 4:08 AM, Sana Saeed wrote:
>> hi gromacs experts
>> i have applied distance, angle and dihedral restraints to my ligand in a protein's pocket so that it doesnt roam around when i turn off all interactions during simulation. do i need to mention about these restraints in the mdp file? i am using gromacs 5.0 and 5.1. i have used intermolecular_interactions directive for defining these restraints.
>
> There is nothing in the .mdp file related to these.
>
>> MY SECOND QUESTION is that the force constant i used is 41.840 kj/mol/K for angle and dihedral restr. does that mean that the Force constant for distance restraint is also 41.840? as i am calculating free energy of restraints (part of absolute binding F.E) so i need force constant for distance also.
>>
>
> The force constant can be whatever you want it to be.
>
> -Justin
>
>
>> [ intermolecular-interactions ]
>> [ distance_restraints ]
>> ;   i     j type label      funct         lo        up1        up2     weight
>>   768  2131 1     0          1   0.640512   0.840512    1.84051          1
>>
>> [ angle_restraints ]
>> ;   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB    multB
>>    770   768    2131  768  1      43.420    0.0   1      43.420   41.840    1
>>    768   2131   2125  2131 1     114.89    0.0   1      114.89   41.840    1
>>
>> [ dihedral_restraints ]
>> ;   ai    aj    ak    al  type    phiA     dphiA  fcA    phiB      dphiB  fcB
>>   782  770   768   2131  1       -152.840  0.0  0.0    -152.840    0.0  41.840
>>   770  768   2131  2125  1       -46.638  0.0  0.0     -46.638     0.0  41.840
>>   768  2131  2125  2132  1       -42.465   0.0  0.0    -42.465     0.0  41.840
>>
>>
>> Sana Saeed Khan,
>> Research Assistant
>> Chemoinformatics Lab
>> Graduate Student, MS bioinfo
>> Department of Bioinformatics
>> Soongsil University, Seoul, South Korea.
>>
>

-- 
==================================================

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

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

==================================================

------------------------------

Message: 4
Date: Wed, 4 May 2016 06:16:46 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] persistent jumps in trajectories
Message-ID: <c53e9f4e-7cc3-2f4b-44b1-61ec7d476297 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

On 5/4/16 6:12 AM, morpheus wrote:
> Hi,
>
> I'm having problems getting jumps out of my trajectories. Usually I follow
> the suggestion of the Gromacs website (
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions)
> and convert my trajectories with the perl script below: remove water, make
> it whole, cluster, nojump, center and fit.
>
> For previous projects these steps always did the job right.
>
> But unfortunately this does not work for long simulations (1500 ns) of
> PDB-ID 2RVD (a peptide of only 10 amino acids). I have performed the
> simulation multiple times and after about 300-500 ns the jumps  still start
> even after processing the trajectories as given below. With jumps I mean
> this: http://s32.postimg.org/z8p90wf51/jump.jpg
>
> Doing analysis on the trajectories with e.g. g_dist yields ?There were 4
> inconsistent shifts. Check your topology?.
>
> I am wondering what I am doing wrong and how can I fix the trajectories?
>
>
> Here is the script that I am usually using:
>
>
> my $bn = $ARGV[0]; # base name
>
> $cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f ".$bn.".md.xtc -s
> ".$bn.".md.tpr -o ".$bn.".noWater.md.xtc -skip 10 << Ende \n1\n1\n << Ende";
>
> system $cmd;
>
>
> $cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f ".$bn.".noWater.md.xtc
> -s ".$bn.".md.tpr -o ".$bn.".noWater.whole.md.xtc -pbc whole << Ende
> \n1\n1\n << Ende";
>
> system $cmd;
>
>
> $cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
> ".$bn.".noWater.whole.md.xtc -s ".$bn.".md.tpr -o
> ".$bn.".noWater.whole.cluster.md.xtc -pbc cluster << Ende \n1\n1\n << Ende";
>
> system $cmd;
>
>
> $cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
> ".$bn.".noWater.whole.cluster.md.xtc -s ".$bn.".md.tpr -o
> ".$bn.".noWater.whole.cluster.nojump.md.xtc -pbc nojump << Ende \n1\n1\n <<
> Ende";
>
> system $cmd;
>
>
> $cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
> ".$bn.".noWater.whole.cluster.nojump.md.xtc -s ".$bn.".md.tpr -o
> ".$bn.".noWater.whole.cluster.nojump.center.md.xtc -center << Ende \n1\n1\n
> << Ende";
>
> system $cmd;
>
>
> $cmd = $execPath.$gPrefix."trjconv".$gPostFix." -f
> ".$bn.".noWater.whole.cluster.nojump.center.md.xtc -s ".$bn.".md.tpr -o
> ".$bn.".final.md.xtc -fit rot+trans << Ende \n1\n1\n << Ende";
>
> system $cmd;
>
>
> Can anyone help?
>

For something as simple as a 10-aa peptide, all you need is:

trjconv -pbc mol -center

Center on the protein and strip the solvent if you like by just selecting 
protein as the output.  Fit afterwards if you need to do so.

-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

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

==================================================

------------------------------

Message: 5
Date: Wed, 04 May 2016 14:32:58 +0200
From: ingram <ingram at fhi-berlin.mpg.de>
To: Gromacs org_gmx users <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] restarts
Message-ID: <266dfa70b2f55412794fd200d46142cf at fhi-berlin.mpg.de>
Content-Type: text/plain; charset=UTF-8; format=flowed

Dear GROMITES

I have run a simulation that will take longer than a day (longer than 
my allowed time for one simulaiton on the cluster)

I ran the command mdrun -deffnm md_golp

Now I'm not sure which .cpt file to use. Two are produced, one called 
state.cpt and one called md_golp.cpt. They are different, but why and 
which one should I use to continue the simulation?

Best

Teresa

------------------------------

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End of gromacs.org_gmx-users Digest, Vol 145, Issue 12
******************************************************