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

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Thu May 5 11:18:35 CEST 2016

```To convert this you need to remember that the square on the nm, which
should then be applied to the 10 A, making 100 A^2:
1000 kJ/(mol nm^2) = 1000 kJ/(mol (10 A)^2)) = 1000 kJ/(mol 100 A^2) =
1000/100 kJ/(mol A^2) = 10 kJ/(mol A^2)

Best wishes
James

> 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
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
>
> On Thursday, May 5, 2016 11:31 AM, Sana Saeed
>
>
>
> Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> 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:
> Send gromacs.org_gmx-users mailing list submissions to
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>
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> 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
>> 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
> 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
>> 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
>>> 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
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
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> End of gromacs.org_gmx-users Digest, Vol 145, Issue 12
> ******************************************************
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```