[gmx-users] Fwd: removing some atoms

[James Lord]

Hi all,

I sent this few days ago and I am still struggling with this, any
help,hints is highly appreciated.




-- Forwarded message --
From: James Lord 
Date: Thu, Nov 26, 2015 at 11:18 PM
Subject: removing some atoms
To: "gmx-us...@gromacs.org" 


Hi all,

I have a oil slab and want to insert a protein so that almost half of the
protein is inserted into the oil and the other half is outside in the
vacuum. Is there any tools in Gromacs so that I can easily remove some of
the oil atoms and make a space for the protein insertion? My apology if it
seems a trivial question.

Cheers,
James
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[gmx-users] removing some atoms

[James Lord]

Hi all,

I have a oil slab and want to insert a protein so that almost half of the
protein is inserted into the oil and the other half is outside in the
vacuum. Is there any tools in Gromacs so that I can easily remove some of
the oil atoms and make a space for the protein insertion? My apology if it
seems a trivial question.

Cheers,
James
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[gmx-users] Fwd: hydrogen bonds

[James Lord]

Hi all,

I am trying to figure out the number of hydrogen bonds between a protein
and membrane and which residues from protein were involved in hydrogen
bonding. I made an index file and selected the protein and membrane,

g_hbond -f md.xtc -s md.tpr -n index.ndx  -num hbond.xvg -hbn  hbond.ndx

the hbond.xvg is giving me the number of hydrogen bonds and as far as I
understood from manual hbond.ndx is should give me the atoms involved but I
am confused seeing the output of hbond.ndx. What are the three columns at
the end (atom numbers involved in hydrogen bonding)? Any comments?


[ hbonds_Protein-MEM ]
  1  2   6407
  1  2   7982
  1  2   7988
161162   4391
201202   4391
201202   4523
201202   5153
201202   5174
201202   5676
201202   5678
253254   3137
266267   3131
266267   5903
275276   3131
275276   5903
279280   3257
279280   3258
279280   3261
279280   3263
279280   5903
279280   5909
279280   8864
301302   2375
310311   3257
310311   3258
310311   3263
310311   3284
316317   3284
323324   2375
323324   2402
323324   3257
323324   3258
323324   3261
323324   3263
323324   3282
323324   3284
323324   5909
323324   6974
323324   6975
323324   6999
323324   7001
323324   8675
323324   8676
323324   8702
323324   8864
323324   8865
323324   8868
323324   8870
323324   8889
323324   8891
332333   2402
332333   8681
332333   8702
332333   8864
332333   8865
332333   8868
332333   8870
332333   8889
332333   8891
336337   2375
336337   2402
364365   2402
367368   2400
367368   2402
367368   8702
370371   2402
370371   8702
606607   8045
606607   8681
606607   8864
606607   8865
606607   8868
606607   8870
606607   8889
606607   8891
630631   8675
630631   8681
630631   8702
974975   7043
987988   6218
987988   6219
987988   6224
987988   6245
   1131   1132   1809
   1131   1132   1833
   1131   1132   3131
   1131   1132   3132
   1131   1132   3135
   1131   1132   3137
   1131   1132   3158
   1131   1132   6407
   1131   1132   6413
   1226   1227   4418
   1226   1227   4517
   1226   1227   6218
   1226   1227   6245
   1238   1239   4418
   1238   1239   4517
   1248   1249   4517
   1248   1249   6224
   1265   1266   6219
   1299   1300   4859
   1339   1340   4859
   1355   1356   3320
   1355   1356   3509
   1355   1356   3510
   1355   1356   3513
   1355   1356   3515
   1355   1356   4017
   1355   1356   4019
   1355   1356   4040
   1355   1356   4838
   1355   1356   7799
   1383   1384   2501
   1383   1384   3137
   1383   1384   3158
   1383   1384   3515
   1383   1384   3536
   1383   1384   4019
   1383   1384   7169
   1383   1384   7799
   1383   1384   7982
   1389   1390   7982
   1395   1396   4013
   1411   1412   3132
   1411   1412   4013
   1411   1412   4019
   1428   1429   1808
   1428   1429   1835
   1428   1429   3131
   1428   1429   3132
   1428   1429   3135
   1428   1429   3137
   1428   1429   3156
   1428   1429   3158
   1428   1429   5930
   1441   1442   3257
   1447   1448   3131
   1447   1448   3132
   1447   1448   4013
   1447   1448   4017
   1447   1448   4019
   1447   1448   4859
   1450   1451   3131
   1450   1451   3132
   1450   1451   3135
   1450   1451   3137
   1450   1451   4013
   1450   1451   4014
   1450   1451   4017
   1450   1451   4019
   1450   1451   4838
   1450   1451   4859
   1453   1454   3131
   1453   1454   3132
   1453   1454   3137
   1453   1454   3156
   1453   1454   4013
   1453   1454   4014
   1453   1454   4017
   1453   1454   4019
   1453   1454   4859
   1467   1468   2375
   1467   1468   2379
   1467   1468   3257
   1467   1468   3258
   1467   1468   3284
   1471   1472   2375
   1471   1472   2379
   1471   1472   3257
   1471   1472   3282
   1471   1472   3284
   1498   1499   4518
   1498   1499   4523
   1498   1499   5090
   1498   1499   6180
   1498   1499   6182
   1510   1511   6182
   1514   1515   4523
   1514   1515   5153
   1514   1515   5174
   1514   1515   6182
   1514   1515   6281
   1514   1515   6287
   1526   1527   4523
   1526   1527   5084
   1526   1527   5085
   1526   1527   5088
   1526   1527   5090
   1526   1527   5111
   1526   1527   5147
   1526   1527   5148
   1526   1527   5151
   1526   1527   5153
   1526   1527   5172
   1526   1527   5174
   1526   1527   6156
   1526   1527   6180
   1526   1527   6182
   1526   

[gmx-users] biphasic simulation and surface-surface tension calculation

[James Lord]

Hi all,

I have done two simulations following Justin's tutorial for biphasic
systems one with cyclohexane-water and the other one with a protein in
water phase that diffuses and comes to the cyclohexane-water interface at
some points and stays there for the rest of simulation. When I calculate
the surface tension as a function of time for cyclohexane-water system it
fluctuates a lot but when I average it over the time of simulation it is
giving me a reasonable value which matches with experimental one. But for
the simulation that I have protein, it is again just giving me the surface
tension of two liquids while I was expecting the surface tension to
decrease upon protein adsorption at interface (this is the case
experimentally, as the protein acts like a surfactant)?  Does anyone have
experience with such a system? any comments is much appreciated.

Here is what I am doing to get surface-surface tension

g_energy -f energy.edr -s md.tpr -o surften.xvg

selecting #Surf*SurfTen when asked


Cheers
James
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Re: [gmx-users] force fields selection

[James Lord]

Hi Antonio,

Thanks for further information and the paper.

Cheers
James

On Thu, Sep 24, 2015 at 3:30 AM, Antonio Baptista 
wrote:

> On Tue, 22 Sep 2015, Justin Lemkul wrote:
>
>
>>
>> On 9/21/15 10:22 PM, James Lord wrote:
>>
>>> Dear gmx users,
>>>
>>> I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein
>>> partitioning at biphasic liquid-liquid interfaces (Similar Justin's
>>> tutorial for biphasic system). Which one is recommended if anyone has
>>> experience with such system and why? appreciate any comments? I know 54a7
>>> is newer version but does it mean it is the best I mean in terms of
>>> reproducing experimental data etc? or is there any well known problems
>>> with
>>> 43a2 for such a system?
>>>
>>>
>> 54a7 corrected a well-known problem in 53a6 with helices being unstable.
>> Previous version (45a3, 43a1, etc) did not have that problem.
>>
>
> If you are concerned with helix stability and/or dynamics, 54a7 is
> probably a good choice. For example, it reproduces the thermodynamics and
> kinetics of a model peptide used in helix nucleation studies:
> http://dx.doi.org/10.1021/ct400529k
>
>
>
>> -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] force fields selection

[James Lord]

Thanks Justin

On Wed, Sep 23, 2015 at 10:42 AM, Justin Lemkul  wrote:

>
>
> On 9/21/15 10:22 PM, James Lord wrote:
>
>> Dear gmx users,
>>
>> I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein
>> partitioning at biphasic liquid-liquid interfaces (Similar Justin's
>> tutorial for biphasic system). Which one is recommended if anyone has
>> experience with such system and why? appreciate any comments? I know 54a7
>> is newer version but does it mean it is the best I mean in terms of
>> reproducing experimental data etc? or is there any well known problems
>> with
>> 43a2 for such a system?
>>
>>
> 54a7 corrected a well-known problem in 53a6 with helices being unstable.
> Previous version (45a3, 43a1, etc) did not have that problem.
>
> -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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> posting!
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[gmx-users] force fields selection

[James Lord]

Dear gmx users,

I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein
partitioning at biphasic liquid-liquid interfaces (Similar Justin's
tutorial for biphasic system). Which one is recommended if anyone has
experience with such system and why? appreciate any comments? I know 54a7
is newer version but does it mean it is the best I mean in terms of
reproducing experimental data etc? or is there any well known problems with
43a2 for such a system?

Cheers
James
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Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field

[James Lord]

Hi Mohsen,

I am struggling with the same problem would you mind if I ask you to send
me your .mdp file ?

Cheers
James


On Tue, Aug 11, 2015 at 4:00 AM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> As an update,
>
> After reading the suggested links I tried two .mdp files which were
> suggested in discussions as solutions. Both worked without any problem on
> my system.
>
> 1) rlist/r(columb/vdw)=(1.4/1.4) , in fact the problem seems to be the
> "twin-range + RF"
> 2) I used "twin-range + RF" BUT I reduced the nstlist to 1, this also works
> for my system.
>
> Thanks for your comments.
> Cheers
> Mohsen
>
> On Tue, Jul 21, 2015 at 4:44 PM, Mohsen Ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
> > I looked at the first link, it was a useful discussion.
> > Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4) and
> > everything is working properly till now.
> > It seems the problem was the "twin-range" + RF with this version of
> > Gromacs as has been discussed and you mentioned already.
> >
> > I am playing a little bit to see if I everything will be fine with the
> > rest of test simulation.
> > I will reply again after my tests.
> >
> > Thanks for the links
> >
> > Cheers
> > Mohsen
> >
> > On Tue, Jul 21, 2015 at 4:21 PM, João M. Damas 
> > wrote:
> >
> >> I really think you may be losing time with LINCS parameters. Look at
> these
> >> links too:
> >>
> >>
> >>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html
> >> http://redmine.gromacs.org/issues/1400
> >>
> >> You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I
> really
> >> think that this may be the source of your problems. The links that I
> sent
> >> you present solutions to your problem, but almost always at a
> >> computational
> >> cost, i.e. slower simulations.
> >>
> >> João
> >>
> >>
> >> On Tue, Jul 21, 2015 at 9:34 PM, V.V.Chaban  wrote:
> >>
> >> > Maybe indeed downgrade to an earlier version.
> >> >
> >> > I, for sure, successfully used reaction field with gromacs 3-3-3
> >> > (imagine when it was).
> >> >
> >> > Professor Vitaly V. Chaban
> >> >
> >> >
> >> >
> >> >
> >> > On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour
> >> >  wrote:
> >> > > Hi Chaban,
> >> > >
> >> > > Me too, but I do not know why starting with the same initial
> >> structures
> >> > and
> >> > > also starting from equilibrated structures again cause LINCS
> problems
> >> in
> >> > one
> >> > > not in the other one.
> >> > >
> >> > > I have tried lincs-iter and lincs-order and also lincs allowable
> angle
> >> > > deviations but LINCS error still exist. This is why I think there is
> >> > > something wrong with other parameters, e.g. reaction field!
> >> > > Sure, I will look at epsilon_r, thanks.
> >> > >
> >> > >
> >> > > On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban 
> >> wrote:
> >> > >>
> >> > >> I do not see much connection between bond constraints and treatment
> >> of
> >> > >> electrostatics beyond the cut-off distance.
> >> > >>
> >> > >> There is also an "epsilon_r" keyword. I would investigate what
> >> exactly
> >> > >> it means and whether it is used in the reaction field procedure.
> >> > >>
> >> > >> The "all-bonds" contraint often results in different problems. You
> >> > >> will have to play with the relevant parameters, like lincs_order
> and
> >> > >> allowable deviation.
> >> > >>
> >> > >>
> >> > >>
> >> > >>
> >> > >>
> >> > >>
> >> > >> On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour
> >> > >>  wrote:
> >> > >> > Dear Gromacs users,
> >> > >> >
> >> > >> > I am interested in simulation of lipid bilayers with Gromos96
> 53a6.
> >> > >> > As I understood this force field has been parametrized with
> >> reaction
> >> > >> > field
> >> > >> > instead of pme.
> >> > >> >
> >> > >> > Based on literatures, I have the following .mdp parameters:
> >> > >> > But I am not sure of those as my system has lots of LINCS
> warnings
> >> > with
> >> > >> > these parameters.
> >> > >> >
> >> > >> > integrator   = md
> >> > >> > tinit   = 0
> >> > >> > dt  = 0.002
> >> > >> > nsteps   = 5
> >> > >> > nstcomm   = 1
> >> > >> > comm-grps=
> >> > >> >
> >> > >> >
> >> > >> > nstxout  = 0
> >> > >> > nstvout  = 0
> >> > >> > nstfout   = 0
> >> > >> > nstenergy= 100
> >> > >> > nstxtcout= 5000
> >> > >> > xtc-precision   = 1000
> >> > >> > energygrps  = system
> >> > >> >
> >> > >> > nstlist  = 5
> >> > >> > ns_type   = grid
> >> > >> > pbc = xyz
> >> > >> > rlist = 0.8
> >> > >> >
> >> > >> > coulombtype = reaction_field
> >> > >> > rcoulomb-switch= 0
> >> > >> > rcoulomb  = 1.4
> >> > >> > epsilon_rf = 62
> >> > >> > vdw-type   

Re: [gmx-users] editconf -density

[James Lord]

Thanks Dan and Mark,
Mark approach gave me I what I wanted.


On Mon, Aug 10, 2015 at 4:43 AM, Mark Abraham 
wrote:

> Hi,
>
> That is unlikely to work for large changes in density, because bond lengths
> get messed up too badly. Instead, you can use Berendsen pressure coupling
> with a larger or smaller target pressure to slowly change the volume in an
> actual simulation. Equilibrate thoroughly afterwards!
>
> Mark
>
> On Sun, 9 Aug 2015 18:27 Dan Sponseller  wrote:
>
> > You do not state your original density. But lets say you need to reduce
> > volume 3% to get your correct density. Use:
> > ediftconf -f solv_large.gro -o solv_large_scaled.gro -scale 1 1 0.97
> >
> > Just do a quick side calculation for what you need and substitute in for
> > 0.97.
> >
> > Dan
> >
> >
> > > On Aug 9, 2015, at 4:18 AM, James Lord 
> wrote:
> > >
> > > Hi all,
> > > I have  a solvent filled in a box of dimensions 12 12 12
> > (solv_large.gro).
> > > I want to adjust the density of system to 824 kg/m3. But I want
> editconf
> > to
> > > just change the volume only by changing the z direction ? is that
> > possible?
> > > I did
> > > ediftconf -f solv_large.gro -o solv_large_scaled.gro -density 824
> > >
> > > But it changes the x,y,z to adjust the density. Is it possible to ask
> > > editconf to do this only by changing for example z?
> > > Cheers
> > > James
> > > --
> > > 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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[gmx-users] editconf -density

[James Lord]

Hi all,
I have  a solvent filled in a box of dimensions 12 12 12 (solv_large.gro).
I want to adjust the density of system to 824 kg/m3. But I want editconf to
just change the volume only by changing the z direction ? is that possible?
I did
ediftconf -f solv_large.gro -o solv_large_scaled.gro -density 824

But it changes the x,y,z to adjust the density. Is it possible to ask
editconf to do this only by changing for example z?
Cheers
James
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[gmx-users] Fwd: Question about editconf -noc flag

[James Lord]

Hi all,
I have made an oil slab (energy minimized, equilibrated nvt and npt), some
of the oil molecules are at the other end (periodicity).
https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs

then I decided to increase the box size in z direction a bit to make enough
room for protein, using

editconf -f OCT_npt.gro -oOCT_newbox.gro -box  6.47271 6.47271 16 -noc

https://drive.google.com/open?id=0B0YMTXH1gmQsT1M3dzBNNTJrT28

I used the last flag to put the oil at the ends of box but it is not doing
for one end? any thoughts?
Cheers
James
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[gmx-users] Question about editconf -noc flag

[James Lord]

Hi all,
I have made an oil slab (energy minimized, equilibrated nvt and npt), some
of the oil molecules are at the other end (periodicity).
https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs

then I decided to increase the box size in z direction a bit to make enough
room for protein, using

editconf -f OCT_npt.gro -oOCT_newbox.gro -box  6.47271 6.47271 16 -noc

https://drive.google.com/file/d/0B0YMTXH1gmQsYmdvQ3huYWtDaGs/view?usp=sharing
I used the last flag to put the oil at the ends of box but it is not doing
for one end? any thoughts?
Cheers
James
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Re: [gmx-users] Question about biphasic tutorial

[James Lord]

Hi Justin,
Welcome back. Thanks I solved it the other day. I got the coordinate and
topology.
Cheers
James

On Monday, July 27, 2015, Justin Lemkul  wrote:

>
>
> On 7/24/15 4:16 AM, James Lord wrote:
>
>> Hi all,
>> I want to make the the hydrophobic layer Justin has made but only have one
>> .itp file from ATB for the hydrophobic layer (no topology and coordinate)?
>> Any suggestion where and how to start to make this  hydrophobic layer? I
>> am
>> aware of what Justin has suggested regarding using PRODRG
>> <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg>,. any comments?
>>
>
> I really don't understand what you're asking.  Can you explain your
> intended process in more detail?
>
> -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] Gromacs Path

[James Lord]

Hi Vikas,
 typing mdrun or which mdrun in your terminal will tell you where it is
installed.
Cheers
James

On Monday, July 27, 2015, Live King  wrote:

> Hi Everyone,
>
> I installed Gromacs-4.6.5 using the command sudo apt-get install gromacs,
> then what is path of my Gromacs directory ? I don't seem to find it
> anywhere .
>
> Thanks,
> vikas
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[gmx-users] Question about biphasic tutorial

[James Lord]

Hi all,
I want to make the the hydrophobic layer Justin has made but only have one
.itp file from ATB for the hydrophobic layer (no topology and coordinate)?
Any suggestion where and how to start to make this  hydrophobic layer? I am
aware of what Justin has suggested regarding using PRODRG
,. any comments?
Cheers
James
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Re: [gmx-users] itp file not found

[James Lord]

Hi All,
Problem solved.
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

Am I the only one missing Justin and his lovely comments??
Cheers
James

On Wed, Jul 22, 2015 at 11:11 PM, James Lord 
wrote:

> Hi all,
> I am running energy minimization and grompp is complaining about following
> error. I am using Gromacs version 4.6.3. On Gromacs website it is saying
> that GROMOS96 54A7 files from ATB website  were added to 4.6.2 and later
> versions right?
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
> <https://webmail.vuw.ac.nz/owa/redir.aspx?SURL=TOLnFV9q38vJudxw-JZkbI7m1r4rIAoHfY4Juci2q9ENk7mUf5LSCGgAdAB0AHAAOgAvAC8AdwB3AHcALgBnAHIAbwBtAGEAYwBzAC4AbwByAGcALwBBAGIAbwB1AHQAXwBHAHIAbwBtAGEAYwBzAC8AUgBlAGwAZQBhAHMAZQBfAE4AbwB0AGUAcwAvAFYAZQByAHMAaQBvAG4AcwBfADQALgA2AC4AeAA.&URL=http%3a%2f%2fwww.gromacs.org%2fAbout_Gromacs%2fRelease_Notes%2fVersions_4.6.x>
>
>   Program grompp, VERSION 4.6.3
> Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293
>
> Fatal error:
> Topology include file "ffG54a7.itp" not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>  My first question is why this .itp file can't be located by grompp?
>
>  I tried to bypass it and downloaded the gromos54a7.ff from ATB (
> GROMOS_54A7_for_Gromacs_4.5.x_5.x.x.tar.gz
> <https://webmail.vuw.ac.nz/owa/redir.aspx?SURL=cxl2s6da--E--3Qm8eDeHLVMVJnO0awk6_wjHfUmuHINk7mUf5LSCGgAdAB0AHAAOgAvAC8AYwBvAG0AcABiAGkAbwAuAGIAaQBvAHMAYwBpAC4AdQBxAC4AZQBkAHUALgBhAHUALwBhAHQAYgAvAGYAbwByAGMAZQBmAGkAZQBsAGQAXwBmAGkAbABlAHMALwBhAHQAYgBfAGcAcgBvAG0AYQBjAHMALwA1AC8AZwByAG8AbQBvAHMANQA0AGEANwBfAGEAdABiAC4AZgBmAC4AdABhAHIALgBnAHoA&URL=http%3a%2f%2fcompbio.biosci.uq.edu.au%2fatb%2fforcefield_files%2fatb_gromacs%2f5%2fgromos54a7_atb.ff.tar.gz>
> )
> and extracted the force field  and put it in my working directory. but
> again grompp is not happy??!!
>
> Program grompp, VERSION 4.6.3
> Source code file: /home/James/gromacs-4.6.3/src/kernel/topio.c, line: 734
>
> Fatal error:
> Syntax error - File forcefield.itp, line 4
> Last line read:
> '[ defaults ]'
> Invalid order for directive defaults
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>  the topology file and the included "decane_G54A7.itp" file in line 4 are
> uploaded. Any thought would be greatly appreciated.
> https://drive.google.com/file/d/0B0YMTXH1gmQscndZcVJxZnZGU2M/view?usp=sharing
> https://drive.google.com/file/d/0B0YMTXH1gmQsVGV0WXBSMU1GbFU/view?usp=sharing
> Cheers
> James
>
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[gmx-users] Fwd: itp file not found

[James Lord]

Hi all,
Sorry apparently my previous emails the shared links just contained one
file, apologize for that.
I am running energy minimization and grompp is complaining about following
error. I am using Gromacs version 4.6.3. On Gromacs website it is saying
that GROMOS96 54A7 files from ATB website  were added to 4.6.2 and later
versions right?
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x


  Program grompp, VERSION 4.6.3
Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293

Fatal error:
Topology include file "ffG54a7.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

 My first question is why this .itp file can't be located by grompp?

 I tried to bypass it and downloaded the gromos54a7.ff from ATB (
GROMOS_54A7_for_Gromacs_4.5.x_5.x.x.tar.gz

)
and extracted the force field  and put it in my working directory. but
again grompp is not happy??!!

Program grompp, VERSION 4.6.3
Source code file: /home/James/gromacs-4.6.3/src/kernel/topio.c, line: 734

Fatal error:
Syntax error - File forcefield.itp, line 4
Last line read:
'[ defaults ]'
Invalid order for directive defaults
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

 the topology file and the included "decane_G54A7.itp" file in line 4 are
uploaded. Any thought would be greatly appreciated.

https://drive.google.com/open?id=0B0YMTXH1gmQscndZcVJxZnZGU2M

https://drive.google.com/open?id=0B0YMTXH1gmQsVGV0WXBSMU1GbFU
Cheers
James
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[gmx-users] Fwd: itp file not found

[James Lord]

Hi all,
I am running energy minimization and grompp is complaining about following
error. I am using Gromacs version 4.6.3. On Gromacs website it is saying
that GROMOS96 54A7 files from ATB website  were added to 4.6.2 and later
versions right?
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x


  Program grompp, VERSION 4.6.3
Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293

Fatal error:
Topology include file "ffG54a7.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

 My first question is why this .itp file can't be located by grompp?

 I tried to bypass it and downloaded the gromos54a7.ff from ATB (
GROMOS_54A7_for_Gromacs_4.5.x_5.x.x.tar.gz

)
and extracted the force field  and put it in my working directory. but
again grompp is not happy??!!

Program grompp, VERSION 4.6.3
Source code file: /home/James/gromacs-4.6.3/src/kernel/topio.c, line: 734

Fatal error:
Syntax error - File forcefield.itp, line 4
Last line read:
'[ defaults ]'
Invalid order for directive defaults
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

 the topology file and the included "decane_G54A7.itp" file in line 4 are
uploaded. Any thought would be greatly appreciated.
https://drive.google.com/file/d/0B0YMTXH1gmQscndZcVJxZnZGU2M/view?usp=sharing


https://drive.google.com/file/d/0B0YMTXH1gmQsVGV0WXBSMU1GbFU/view?usp=sharing

Cheers
James
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[gmx-users] itp file not found

[James Lord]

 Hi all,
I am running energy minimization and grompp is complaining about following
error. I am using Gromacs version 4.6.3. On Gromacs website it is saying
that GROMOS96 54A7 files from ATB website  were added to 4.6.2 and later
versions right?
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x


  Program grompp, VERSION 4.6.3
Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293

Fatal error:
Topology include file "ffG54a7.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

 My first question is why this .itp file can't be located by grompp?

 I tried to bypass it and downloaded the gromos54a7.ff from ATB (
GROMOS_54A7_for_Gromacs_4.5.x_5.x.x.tar.gz

)
and extracted the force field  and put it in my working directory. but
again grompp is not happy??!!

Program grompp, VERSION 4.6.3
Source code file: /home/James/gromacs-4.6.3/src/kernel/topio.c, line: 734

Fatal error:
Syntax error - File forcefield.itp, line 4
Last line read:
'[ defaults ]'
Invalid order for directive defaults
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

 the topology file and the included "decane_G54A7.itp" file in line 4 are
uploaded. Any thought would be greatly appreciated.
https://drive.google.com/file/d/0B0YMTXH1gmQscndZcVJxZnZGU2M/view?usp=sharing
https://drive.google.com/file/d/0B0YMTXH1gmQsVGV0WXBSMU1GbFU/view?usp=sharing
Cheers
James
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Re: [gmx-users] GPU gromacs

[James Lord]

Thanks Slizard. I need to get this simulation done in a week but does not
have the right facilities. Is there anyone in the group with some high end
GPU cards that can help me get this running.
Cheers
James

On Tuesday, July 7, 2015, Szilárd Páll  wrote:

> Of course you can, but with such a low-end mobile GPU you may not even gain
> performance from offloading computation from the CPU and additionally you
> may have issues with cooling too.
>
> You can simply try comparing performance with "-nb cpu" and "-nb gpu" to
> see if using the GPU improves performance at all.
>
> --
> Szilárd
>
> On Sat, Jul 4, 2015 at 1:40 PM, James Lord  > wrote:
>
> > Hi All,
> > I have a system with 300k atoms, I don't have access to HPC facilities,
> Is
> > it possible to run gromcas on GPU on a desktop with following graphic
> card
> > for up to 200-300 ns?
> >
> > 00:02.0 VGA compatible controller: Intel Corporation 3rd Gen Core
> processor
> > Graphics Controller (rev 09)
> > 01:00.0 VGA compatible controller: NVIDIA Corporation GF108M [GeForce GT
> > 635M] (rev a1)
> >
> > any thoughts is greatly appreciated.
> > Cheers
> > James
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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> >
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Re: [gmx-users] Question regarding box size

[James Lord]

Thanks Justin and Victor

On Sat, Jul 11, 2015 at 9:12 AM, Justin Lemkul  wrote:

>
>
> On 7/10/15 1:35 AM, James Lord wrote:
>
>> Hi all,
>> I have a system with 300k atoms, but computationally it is expensive for
>> me
>> doing simulation with such a big system, Is it possible to reduce the box
>> size? If yes how? (the .gro file is uploaded). I know from Justin tutorial
>> genconf
>> -nboxvector 1 1 1
>> Does the numbers after -nbox have to  integer?
>>
>> The size of box required to contain protein with 1.5nm of water on each
>> side. Sorry I could not figure it out what to do and how to tackle this
>> simple task. re bulding the simulation from scratch is an option but
>> thought might find quicker and smarter way here. I want to have optimum
>> size in each direction so that the protein does not see its periodic
>> image.
>> Appreciate any specific thoughts on my system and the box size I have got
>> now.
>>
>>
>> https://drive.google.com/file/d/0B0YMTXH1gmQsdFVKWkdPLURCUVk/view?usp=sharing
>>
>>
> Given that you have a large protein and you're creating a biphasic system,
> there's not much you can do.  The water box may be a bit large along z, but
> that's about all you can likely change here.
>
> -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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[gmx-users] Question regarding box size

[James Lord]

Hi all,
I have a system with 300k atoms, but computationally it is expensive for me
doing simulation with such a big system, Is it possible to reduce the box
size? If yes how? (the .gro file is uploaded). I know from Justin tutorial
genconf
-nboxvector 1 1 1
Does the numbers after -nbox have to  integer?

The size of box required to contain protein with 1.5nm of water on each
side. Sorry I could not figure it out what to do and how to tackle this
simple task. re bulding the simulation from scratch is an option but
thought might find quicker and smarter way here. I want to have optimum
size in each direction so that the protein does not see its periodic image.
Appreciate any specific thoughts on my system and the box size I have got
now.

https://drive.google.com/file/d/0B0YMTXH1gmQsdFVKWkdPLURCUVk/view?usp=sharing

Cheers
James
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[gmx-users] GPU gromacs

[James Lord]

Hi All,
I have a system with 300k atoms, I don't have access to HPC facilities, Is
it possible to run gromcas on GPU on a desktop with following graphic card
for up to 200-300 ns?

00:02.0 VGA compatible controller: Intel Corporation 3rd Gen Core processor
Graphics Controller (rev 09)
01:00.0 VGA compatible controller: NVIDIA Corporation GF108M [GeForce GT
635M] (rev a1)

any thoughts is greatly appreciated.
Cheers
James
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Re: [gmx-users] Biphasic Systems for BSA

[James Lord]

Thanks heaps Justin

On Sun, Jun 28, 2015 at 1:58 PM, Justin Lemkul  wrote:

>
>
> On 6/27/15 9:48 PM, James Lord wrote:
>
>> Hi Justin,
>> Thanks for your email. Would you please tell me how I can do this? Sorry
>> to
>> bother you. below is the PBD I generated with Swiss-PdbViewr.
>>
>> https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view
>>
>>
> This is very simple with standard Linux command-line tools, e.g. to get
> monomer chain A:
>
> grep " A " 3V03.pdb | grep "ATOM\|HETATM" > chainA.pdb
>
>
> -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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Re: [gmx-users] Biphasic Systems for BSA

[James Lord]

Hi Justin,
Thanks for your email. Would you please tell me how I can do this? Sorry to
bother you. below is the PBD I generated with Swiss-PdbViewr.

https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view


On Sun, Jun 28, 2015 at 11:47 AM, Justin Lemkul  wrote:

>
>
> On 6/27/15 7:46 PM, James Lord wrote:
>
>> Hi Justin & Tsjerk,
>> Thanks for the info,
>> Tsjerk: I was looking for the monomer but could not find monomer structure
>> on protein data bank.
>>
>
> Because it crystallizes as a dimer.  The state in the crystal is not
> necessarily what one finds in solution.  Just pull a single chain out of
> the PDB file.
>
>
> -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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>
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Re: [gmx-users] Biphasic Systems for BSA

[James Lord]

Hi Justin & Tsjerk,
Thanks for the info,
Tsjerk: I was looking for the monomer but could not find monomer structure
on protein data bank.
Cheers
James

On Sun, Jun 28, 2015 at 6:50 AM, Tsjerk Wassenaar  wrote:

> Hi,
>
> Actually no, you may be better off with a hexagonal prism, or even a
> rhombic dodecahedron, which has a hexagonal base too.
>
> Oh, and that structure of BSA is a dimer, while the biological unit is a
> monomer...
>
> Cheers,
>
> Tsjerk
> On Jun 27, 2015 7:20 PM, "Justin Lemkul"  wrote:
>
> >
> >
> > On 6/27/15 2:38 AM, James Lord wrote:
> >
> >> Hi all,
> >> I have a trivial question, What is the best box type and size for a big
> >> protein such as BSA (attached .pdb) to minimize computational cost? what
> >> is
> >> the rule of thumb re the protein distance to box wall?
> >> This protein is around 16 nm in x direction and 6nm in y.
> >>
> >>
> https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view?usp=sharing
> >>
> >>
> > If, as your subject line implies, you are setting up a layered system,
> you
> > are largely stuck with a rectangular box.  The dimensions can easily be
> > determined by setting up the protein in a cubic box with editconf and
> > conventional solute-box distances.  That distance depends on the force
> > field (viz. the required cutoffs), to avoid minimum-image violations.
> This
> > is all very rudimentary stuff and is covered by tutorials and MD texts.
> >
> > -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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> >
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> >
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[gmx-users] Biphasic Systems for BSA

[James Lord]

Hi all,
I have a trivial question, What is the best box type and size for a big
protein such as BSA (attached .pdb) to minimize computational cost? what is
the rule of thumb re the protein distance to box wall?
This protein is around 16 nm in x direction and 6nm in y.
https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view?usp=sharing

Cheers
James
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Re: [gmx-users] energy minimization error

[James Lord]

Hi Justin
For now I  used


*mdrun -nt 1*


* and got rid of this error so hopefully the simulation wont crash. *

*Cheers*

*James*


On Sat, Jun 27, 2015 at 11:19 AM, James Lord 
wrote:

> Hi Justin,
> I have asked this before, but this time I started up from scratch and used
> the input files that I know they are fine but again I am getting this
> error, Would you please tell me what is wrong in my topology files and
> where about in .top files the bond length are defined?
>
>
> https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing
>
> Cheers
> James
>
> On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/16/15 11:35 PM, James Lord wrote:
>>
>>> Hi Justin
>>> Thanks for this. Can you tell me which step(s) this bond length is
>>> defined
>>> What should I do (redo) to resolve this issue?
>>>
>>
>> The bonds are defined in the topology.  The DD algorithm reads what's in
>> the coordinate file and builds cells based on the geometry it finds there.
>>
>> Without a full description of what's in your system, what steps you've
>> taken to prepare it (full commands, in order), there's little I can suggest
>> because it would all be guesswork.
>>
>>
>> -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
>>
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>> 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] energy minimization error

[James Lord]

Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?

https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing

Cheers
James

On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul  wrote:

>
>
> On 5/16/15 11:35 PM, James Lord wrote:
>
>> Hi Justin
>> Thanks for this. Can you tell me which step(s) this bond length is
>> defined
>> What should I do (redo) to resolve this issue?
>>
>
> The bonds are defined in the topology.  The DD algorithm reads what's in
> the coordinate file and builds cells based on the geometry it finds there.
>
> Without a full description of what's in your system, what steps you've
> taken to prepare it (full commands, in order), there's little I can suggest
> because it would all be guesswork.
>
>
> -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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>
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Re: [gmx-users] energy minimization error

[James Lord]

Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is
defined What should I do (redo) to resolve this issue?
Cheers
James

On Sun, May 17, 2015 at 9:02 AM, Justin Lemkul  wrote:

>
>
> On 5/16/15 6:27 AM, James Lord wrote:
>
>> Dear gmx users,
>> I am getting this error, Can anyone help me to get around this?
>> Cheers
>> James
>>
>>
>> Program mdrun, VERSION 4.6.3
>> Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792
>>
>> Fatal error:
>> There is no domain decomposition for 8 nodes that is compatible with the
>> given box and a minimum cell size of 6.93203 nm
>> Change the number of nodes or mdrun option -rdd
>> Look in the log file for details on the domain decomposition
>>
>>
>>
>> Log file opened on Sat May 16 22:15:44 2015
>> Host: james-E530  pid: 22300  nodeid: 0  nnodes:  1
>> Gromacs version:VERSION 4.6.3
>> Precision:  single
>> Memory model:   64 bit
>> MPI library:thread_mpi
>> OpenMP support: enabled
>> GPU support:disabled
>> invsqrt routine:gmx_software_invsqrt(x)
>> CPU acceleration:   AVX_256
>> FFT library:fftw-3.3.2-sse2
>> Large file support: enabled
>> RDTSCP usage:   enabled
>> Built on:   Wed Oct 30 18:28:46 NZDT 2013
>> Built by:   james@james-E530 [CMAKE]
>> Build OS/arch:  Linux 3.11.0-12-generic x86_64
>> Build CPU vendor:   GenuineIntel
>> Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz
>> Build CPU family:   6   Model: 58   Stepping: 9
>> Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
>> nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1
>> sse4.2 ssse3 tdt x2apic
>> C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8)
>> 4.8.1
>> C compiler flags:   -mavx-Wextra -Wno-missing-field-initializers
>> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter
>> -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
>> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
>> -DNDEBUG
>>
>>
>>   :-)  G  R  O  M  A  C  S  (-:
>>
>>Gromacs Runs On Most of All Computer Systems
>>
>>  :-)  VERSION 4.6.3  (-:
>>
>>  Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
>> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
>>   Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph
>> Junghans,
>>  Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>>  Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>
>> Berk Hess, David van der Spoel, and Erik Lindahl.
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>   Copyright (c) 2001-2012,2013, The GROMACS development team at
>>  Uppsala University & The Royal Institute of Technology, Sweden.
>>  check out http://www.gromacs.org for more information.
>>
>>   This program is free software; you can redistribute it and/or
>> modify it under the terms of the GNU Lesser General Public License
>>  as published by the Free Software Foundation; either version 2.1
>>   of the License, or (at your option) any later version.
>>
>>  :-)  mdrun  (-:
>>
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
>> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
>> molecular simulation
>> J. Chem. Theory Comput. 4 (2008) pp. 435-447
>>   --- Thank You ---  
>>
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J.
>> C.
>> Berendsen
>> GROMACS: Fast, Flexible and Free
>> J. Comp. Chem. 26 (2005) pp. 1701-1719
>>   --- Thank You ---  
>>
>>
>>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
>> E. Lindahl and B. Hess and D. van der Spoel
>> GROMACS 3.0: A package for molecular simulation and trajectory analysis
>> J. Mol. Mod. 7 (2001) pp. 306-317
>>   --- Thank You ---  
>>
>>

[gmx-users] energy minimization error

[James Lord]

Dear gmx users,
I am getting this error, Can anyone help me to get around this?
Cheers
James


Program mdrun, VERSION 4.6.3
Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 6.93203 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition



Log file opened on Sat May 16 22:15:44 2015
Host: james-E530  pid: 22300  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6.3
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Wed Oct 30 18:28:46 NZDT 2013
Built by:   james@james-E530 [CMAKE]
Build OS/arch:  Linux 3.11.0-12-generic x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz
Build CPU family:   6   Model: 58   Stepping: 9
Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1
C compiler flags:   -mavx-Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter
-Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
-DNDEBUG


 :-)  G  R  O  M  A  C  S  (-:

  Gromacs Runs On Most of All Computer Systems

:-)  VERSION 4.6.3  (-:

Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
   Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
 Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
 of the License, or (at your option) any later version.

:-)  mdrun  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  

Input Parameters:
   integrator   = steep
   nsteps   = 5
   init-step= 0
   cutoff-scheme= Group
   ns_type  = Grid
   nstlist  = 5
   ndelta   = 2
   nstcomm  = 100
   comm-mode= Linear
   nstlog   = 1000
   nstxout  = 0
   nstvout  = 0
   nstfout  = 0
   nstcalcenergy= 100
   nstenergy= 1000
   nstxtcout= 0
   init-t   = 0
   delta-t  = 0.001
   xtcprec  = 1000
   fourierspacing   = 0.12
   nkx  = 56
   nky  = 56
   nkz  = 144
   pme-order= 4
   ewald-rtol   = 1e-05
   ewald-geometry   = 0
   epsilon-surface  = 0
   optimize-fft = FALSE
   ePBC = xyz
   bPeriodicMols 

[gmx-users] warnings in energy minimization

[James Lord]

Hi all,
I am using Justin's minim.mdp to energy minimize my system and I am getting
these warnings,Should I care about them? It is saying that my simulation
may not be stable?

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5

WARNING: Listed nonbonded interaction between particles 5312 and 5315
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
Cheers
James
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Re: [gmx-users] genion error sol not continuous

[James Lord]

Thanks Justin problem solved.
Cheers
James

On Sat, May 16, 2015 at 9:21 AM, Justin Lemkul  wrote:

>
>
> On 5/15/15 4:53 PM, James Lord wrote:
>
>> Hi Justin,
>> Thanks for your email. I have modified it and the topology looks fine to
>> me or
>> at least I can't see any problem with it but still genion does not like
>> it?
>> Would please have a look?
>>
>> https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing
>>
>> https://drive.google.com/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing
>>
>>
> I don't know what I'm supposed to be looking at, and without the chain
> topologies it's impossible to troubleshoot.  Please upload a *complete*
> archive (.tgz) of all files (coordinates, topologies - .top and .itp, force
> field, etc) needed to execute grompp to reproduce the problem.  Also
> provide the exact command you're issuing.
>
>
> -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
>
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Re: [gmx-users] genion error sol not continuous

[James Lord]

Hi Justin,
Thanks for your email. I have modified it and the topology looks fine to me
or at least I can't see any problem with it but still genion does not like
it? Would please have a look?
https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing
https://drive.google.com/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing

Thanks
James

On Fri, May 15, 2015 at 4:36 AM, Justin Lemkul  wrote:

>
>
> On 5/14/15 1:25 AM, James Lord wrote:
>
>> Hi all,
>> I am trying to neutralize this system (1HFX.gro) and genion is complaining
>> about solvent not being continuous,then I made the 1HFX_modified.gro in
>> which
>> I have replaced HOH from 1HFX.gro with SOL and cut paste them at the end
>> of
>> the file. I am expecting gromacs to do the reordering for SOL. Am I
>> missing
>> anything?
>>
>
> The topology needs to be modified in a similar manner.  IIRC it is
> topological continuity that genion checks.
>
> -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
>
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> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] genion error sol not continuous

[James Lord]

Hi all,
I am trying to neutralize this system (1HFX.gro) and genion is complaining
about solvent not being continuous,then I made the 1HFX_modified.gro in
which
I have replaced HOH from 1HFX.gro with SOL and cut paste them at the end of
the file. I am expecting gromacs to do the reordering for SOL. Am I missing
anything?
The 1HFX_modified.gro looks fine to me but keep giving the error. Any
comments?

https://drive.google.com/file/d/0B0YMTXH1gmQsTHR0NXhfNWk1SDA/view?usp=sharing
https://drive.google.com/file/d/0B0YMTXH1gmQsVHFDQUgwamwtRW8/view?usp=sharing

Cheers
James
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Re: [gmx-users] Gromacs in UBUNTU

[James Lord]

Hi Saeed,
You don't necessarily need to install it first from Ubuntu software center
and then update it. you can directly get the latest version and follow the
instruction on gromacs website.
Quick and dirty installation


   1. Get the latest version of your C and C++ compilers.
   2. Check that you have CMake version 2.8.8 or later.
   3. Get and unpack the latest version of the GROMACS tarball.
   4. Make a separate build directory and change to it.
   5. Run cmake with the path to the source as an argument
   6. Run make, make check, and make install

Or, as a sequence of commands to execute:

tar xfz gromacs-5.0.5.tar.gz
cd gromacs-5.0.5
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Cheers

James


On Thu, May 14, 2015 at 1:53 PM, saeed poorasad 
wrote:

> Dear Gromacs users ,
> Greetings .I want to install Gromacs with using of UBUNTU software center
> .  Now I want to know about updating process of this version of gromacs
> . Does it update automatically with Ubuntu ?
> Thanks for your attention .Best,Saeed.
> --
> 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
>
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Re: [gmx-users] total charge (qtot)

[James Lord]

ops silly one though, I meant just need to select solvent when asked right?

On Thu, May 14, 2015 at 1:13 PM, James Lord 
wrote:

> Thanks Justin,
>>
>> So Just adding +7 Na to the whole system should be good to go to next
>> step? or do I need to neutralize each chain separately? If yes how?
>
> Cheers
> James
>
> On Thu, May 14, 2015 at 1:05 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/13/15 9:04 AM, James Lord wrote:
>>
>>> Dear gmx users,
>>> I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb,
>>>
>>>
>>> https://drive.google.com/file/d/0B0YMTXH1gmQsUjVSd01ERXVpLTA/view?usp=sharing
>>>
>>> I would like to know the total charge of my system but I have two
>>> statement
>>> for that,after running
>>>
>>> pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
>>>
>>>   one is saying -9e and 2e? I am a bit confuse can anyone tell me why it
>>> is
>>> like this? I also checked the topol.top and there is no "qtot"
>>>
>>>
>> You have multiple chains, each with a net charge.  The qtot value is, in
>> fact, printed to the topology, just in each chain's .itp file.
>>
>> -Justin
>>
>>
>>
>>> pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
>>>   :-)  G  R  O  M  A  C  S  (-:
>>>
>>>   Good ROcking Metal Altar for Chronical Sinners
>>>
>>>  :-)  VERSION 4.6.3  (-:
>>>
>>>  Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
>>> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
>>>   Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph
>>> Junghans,
>>>  Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
>>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>>>  Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>>
>>> Berk Hess, David van der Spoel, and Erik Lindahl.
>>>
>>> Copyright (c) 1991-2000, University of Groningen, The
>>> Netherlands.
>>>   Copyright (c) 2001-2012,2013, The GROMACS development team at
>>>  Uppsala University & The Royal Institute of Technology, Sweden.
>>>  check out http://www.gromacs.org for more information.
>>>
>>>   This program is free software; you can redistribute it and/or
>>> modify it under the terms of the GNU Lesser General Public
>>> License
>>>  as published by the Free Software Foundation; either version 2.1
>>>   of the License, or (at your option) any later version.
>>>
>>> :-)  pdb2gmx  (-:
>>>
>>> Option Filename  Type Description
>>> 
>>>-f   1HFX.pdb  InputStructure file: gro g96 pdb tpr etc.
>>>-o 1HFX_processed.gro  Output   Structure file: gro g96 pdb etc.
>>>-p  topol.top  Output   Topology file
>>>-i  posre.itp  Output   Include file for topology
>>>-n  clean.ndx  Output, Opt. Index file
>>>-q  clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.
>>>
>>> Option   Type   Value   Description
>>> --
>>> -[no]h   bool   no  Print help info and quit
>>> -[no]version bool   no  Print version info and quit
>>> -niceint0   Set the nicelevel
>>> -chainsepenum   id_or_ter  Condition in PDB files when a new chain
>>> should
>>>  be started (adding termini): id_or_ter,
>>>  id_and_ter, ter, id or interactive
>>> -merge   enum   no  Merge multiple chains into a single
>>>  [moleculetype]: no, all or interactive
>>> -ff  string select  Force field, interactive by default. Use -h
>>> for
>>>  information.
>>> -water   enum   spceWater model to use: select, none, spc, spce,
>>>  tip3p, tip4p or tip5p
>>> -[no]inter   bool   no  Set the next 8 options to interactive
>>> -[no]ss  bool   no  Interactive SS bridge selection
>>> -[no]ter bool   no  Interactive termini sele

Re: [gmx-users] total charge (qtot)

[James Lord]

Thanks Justin,
>
> So Just adding +7 Na to the whole system should be good to go to next
> step? or do I need to neutralize each chain separately? If yes how?

Cheers
James

On Thu, May 14, 2015 at 1:05 AM, Justin Lemkul  wrote:

>
>
> On 5/13/15 9:04 AM, James Lord wrote:
>
>> Dear gmx users,
>> I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb,
>>
>>
>> https://drive.google.com/file/d/0B0YMTXH1gmQsUjVSd01ERXVpLTA/view?usp=sharing
>>
>> I would like to know the total charge of my system but I have two
>> statement
>> for that,after running
>>
>> pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
>>
>>   one is saying -9e and 2e? I am a bit confuse can anyone tell me why it
>> is
>> like this? I also checked the topol.top and there is no "qtot"
>>
>>
> You have multiple chains, each with a net charge.  The qtot value is, in
> fact, printed to the topology, just in each chain's .itp file.
>
> -Justin
>
>
>
>> pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
>>   :-)  G  R  O  M  A  C  S  (-:
>>
>>   Good ROcking Metal Altar for Chronical Sinners
>>
>>  :-)  VERSION 4.6.3  (-:
>>
>>  Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
>> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
>>   Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph
>> Junghans,
>>  Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>>  Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>
>> Berk Hess, David van der Spoel, and Erik Lindahl.
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>   Copyright (c) 2001-2012,2013, The GROMACS development team at
>>  Uppsala University & The Royal Institute of Technology, Sweden.
>>  check out http://www.gromacs.org for more information.
>>
>>   This program is free software; you can redistribute it and/or
>> modify it under the terms of the GNU Lesser General Public License
>>  as published by the Free Software Foundation; either version 2.1
>>   of the License, or (at your option) any later version.
>>
>> :-)  pdb2gmx  (-:
>>
>> Option Filename  Type Description
>> 
>>-f   1HFX.pdb  InputStructure file: gro g96 pdb tpr etc.
>>-o 1HFX_processed.gro  Output   Structure file: gro g96 pdb etc.
>>-p  topol.top  Output   Topology file
>>-i  posre.itp  Output   Include file for topology
>>-n  clean.ndx  Output, Opt. Index file
>>-q  clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.
>>
>> Option   Type   Value   Description
>> --
>> -[no]h   bool   no  Print help info and quit
>> -[no]version bool   no  Print version info and quit
>> -niceint0   Set the nicelevel
>> -chainsepenum   id_or_ter  Condition in PDB files when a new chain
>> should
>>  be started (adding termini): id_or_ter,
>>  id_and_ter, ter, id or interactive
>> -merge   enum   no  Merge multiple chains into a single
>>  [moleculetype]: no, all or interactive
>> -ff  string select  Force field, interactive by default. Use -h
>> for
>>  information.
>> -water   enum   spceWater model to use: select, none, spc, spce,
>>  tip3p, tip4p or tip5p
>> -[no]inter   bool   no  Set the next 8 options to interactive
>> -[no]ss  bool   no  Interactive SS bridge selection
>> -[no]ter bool   no  Interactive termini selection, instead of
>> charged
>>  (default)
>> -[no]lys bool   no  Interactive lysine selection, instead of
>> charged
>> -[no]arg bool   no  Interactive arginine selection, instead of
>> charged
>> -[no]asp bool   no  Interactive aspartic acid selection, instead
>> of
>>  charged
>> -[no]glu bool   no  Interactive glutamic acid selection, instead
>> of
>> 

Re: [gmx-users] total charge (qtot)

[James Lord]

I can see that I have two chains but can I simply say the total charge is
-7 e?
Cheers
James

On Thu, May 14, 2015 at 1:04 AM, James Lord 
wrote:

> Dear gmx users,
> I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb,
>
>
> https://drive.google.com/file/d/0B0YMTXH1gmQsUjVSd01ERXVpLTA/view?usp=sharing
>
> I would like to know the total charge of my system but I have two
> statement for that,after running
>
> pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
>
>  one is saying -9e and 2e? I am a bit confuse can anyone tell me why it is
> like this? I also checked the topol.top and there is no "qtot"
>
>
> pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
>  :-)  G  R  O  M  A  C  S  (-:
>
>  Good ROcking Metal Altar for Chronical Sinners
>
> :-)  VERSION 4.6.3  (-:
>
> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
>Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
>  Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
>Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>Berk Hess, David van der Spoel, and Erik Lindahl.
>
>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>  Copyright (c) 2001-2012,2013, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>modify it under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
>  of the License, or (at your option) any later version.
>
>:-)  pdb2gmx  (-:
>
> Option Filename  Type Description
> 
>   -f   1HFX.pdb  InputStructure file: gro g96 pdb tpr etc.
>   -o 1HFX_processed.gro  Output   Structure file: gro g96 pdb etc.
>   -p  topol.top  Output   Topology file
>   -i  posre.itp  Output   Include file for topology
>   -n  clean.ndx  Output, Opt. Index file
>   -q  clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -[no]version bool   no  Print version info and quit
> -niceint0   Set the nicelevel
> -chainsepenum   id_or_ter  Condition in PDB files when a new chain
> should
> be started (adding termini): id_or_ter,
> id_and_ter, ter, id or interactive
> -merge   enum   no  Merge multiple chains into a single
> [moleculetype]: no, all or interactive
> -ff  string select  Force field, interactive by default. Use -h for
> information.
> -water   enum   spceWater model to use: select, none, spc, spce,
> tip3p, tip4p or tip5p
> -[no]inter   bool   no  Set the next 8 options to interactive
> -[no]ss  bool   no  Interactive SS bridge selection
> -[no]ter bool   no  Interactive termini selection, instead of
> charged
> (default)
> -[no]lys bool   no  Interactive lysine selection, instead of
> charged
> -[no]arg bool   no  Interactive arginine selection, instead of
> charged
> -[no]asp bool   no  Interactive aspartic acid selection, instead of
> charged
> -[no]glu bool   no  Interactive glutamic acid selection, instead of
> charged
> -[no]gln bool   no  Interactive glutamine selection, instead of
> neutral
> -[no]his bool   no  Interactive histidine selection, instead of
> checking H-bonds
> -angle   real   135 Minimum hydrogen-donor-acceptor angle for a
> H-bond (degrees)
> -distreal   0.3 Maximum donor-acceptor distance for a H-bond
> (nm)
> -[no]una bool   no  Select aromatic rings with united CH atoms on
> phenylalanine, tryptophane and tyrosine
> -[no]ignhbool   no  Ignore hydrogen atoms that are in the
> coordinate
>  

[gmx-users] total charge (qtot)

[James Lord]

Dear gmx users,
I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb,

https://drive.google.com/file/d/0B0YMTXH1gmQsUjVSd01ERXVpLTA/view?usp=sharing

I would like to know the total charge of my system but I have two statement
for that,after running

pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce

 one is saying -9e and 2e? I am a bit confuse can anyone tell me why it is
like this? I also checked the topol.top and there is no "qtot"


pdb2gmx -f 1HFX.pdb -o 1HFX_processed.gro -water spce
 :-)  G  R  O  M  A  C  S  (-:

 Good ROcking Metal Altar for Chronical Sinners

:-)  VERSION 4.6.3  (-:

Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
   Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
 Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
 of the License, or (at your option) any later version.

   :-)  pdb2gmx  (-:

Option Filename  Type Description

  -f   1HFX.pdb  InputStructure file: gro g96 pdb tpr etc.
  -o 1HFX_processed.gro  Output   Structure file: gro g96 pdb etc.
  -p  topol.top  Output   Topology file
  -i  posre.itp  Output   Include file for topology
  -n  clean.ndx  Output, Opt. Index file
  -q  clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-chainsepenum   id_or_ter  Condition in PDB files when a new chain
should
be started (adding termini): id_or_ter,
id_and_ter, ter, id or interactive
-merge   enum   no  Merge multiple chains into a single
[moleculetype]: no, all or interactive
-ff  string select  Force field, interactive by default. Use -h for
information.
-water   enum   spceWater model to use: select, none, spc, spce,
tip3p, tip4p or tip5p
-[no]inter   bool   no  Set the next 8 options to interactive
-[no]ss  bool   no  Interactive SS bridge selection
-[no]ter bool   no  Interactive termini selection, instead of
charged
(default)
-[no]lys bool   no  Interactive lysine selection, instead of charged
-[no]arg bool   no  Interactive arginine selection, instead of
charged
-[no]asp bool   no  Interactive aspartic acid selection, instead of
charged
-[no]glu bool   no  Interactive glutamic acid selection, instead of
charged
-[no]gln bool   no  Interactive glutamine selection, instead of
neutral
-[no]his bool   no  Interactive histidine selection, instead of
checking H-bonds
-angle   real   135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-distreal   0.3 Maximum donor-acceptor distance for a H-bond
(nm)
-[no]una bool   no  Select aromatic rings with united CH atoms on
phenylalanine, tryptophane and tyrosine
-[no]ignhbool   no  Ignore hydrogen atoms that are in the coordinate
file
-[no]missing bool   no  Continue when atoms are missing, dangerous
-[no]v   bool   no  Be slightly more verbose in messages
-posrefc real   1000Force constant for position restraints
-vsite   enum   noneConvert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh  bool   no  Make hydrogen atoms heavy
-[no]deuterate bool no  Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes Use charge groups in the .rtp file
-[no]cmapbool   yes Use cmap torsions (if enabled in the .rtp file)
-[no]renum   bool   no  Renumber t

Re: [gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

[James Lord]

Thanks Justin.

On Wed, May 13, 2015 at 11:33 PM, Justin Lemkul  wrote:

>
>
> On 5/13/15 6:16 AM, James Lord wrote:
>
>> Many thanks Justin,
>> I created a new .pdb file with SwissPDBViewr  but again executing pbd2gmx
>> is
>> giving the following warning and error
>>
>>
>> Warning: Starting residue CA584 in chain not identified as
>> Protein/RNA/DNA.
>> Warning: Starting residue CA585 in chain not identified as
>> Protein/RNA/DNA.
>> Warning: Starting residue CA586 in chain not identified as
>> Protein/RNA/DNA.
>> Warning: Starting residue ACT587 in chain not identified as
>> Protein/RNA/DNA.
>> Problem with chain definition, or missing terminal residues.
>> This chain does not appear to contain a recognized chain molecule.
>> If this is incorrect, you can edit residuetypes.dat to modify the
>> behavior.
>> 8 out of 8 lines of specbond.dat converted successfully
>>
>> ---
>> Program pdb2gmx, VERSION -4.5.4
>> Source code file: /home/James/gromacs-4.5.4/src/kernel/resall.c, line: 642
>>
>> Fatal error:
>> Residue 'ACT' not found in residue topology database
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> Here is the link to new PDB, my question is what is ACT residue? and how
>> to
>>
>
> Did you read the contents of the PDB file?
>
> REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CA ACETATE, 20% PEG3350, 0.1 M
> REMARK 280  TRIS HCL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
> 289K
>
> If you visualize ACT you will see it is acetate.
>
>  resolve this issue, any thought is greatly appreciated?
>>
>
> Given that it's a crystallization co-solvent it's unlikely to be
> functional in any way, so you can likely delete 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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

[James Lord]

Many thanks Justin,
I created a new .pdb file with SwissPDBViewr  but again executing pbd2gmx
is giving the following warning and error


Warning: Starting residue CA584 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue CA585 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue CA586 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue ACT587 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

---
Program pdb2gmx, VERSION -4.5.4
Source code file: /home/James/gromacs-4.5.4/src/kernel/resall.c, line: 642

Fatal error:
Residue 'ACT' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Here is the link to new PDB, my question is what is ACT residue? and how to
resolve this issue, any thought is greatly appreciated?
https://drive.google.com/file/d/0B0YMTXH1gmQsSWlXTU56R0FYcVk/view?usp=sharing

Cheers
James


On Sat, May 9, 2015 at 12:26 PM, Justin Lemkul  wrote:

>
>
> On 5/9/15 3:13 AM, James Lord wrote:
>
>> Hi Justin,
>> I opened up the strucutre in Swissviewr. Then how can I have a pdb with
>> missing
>> parts added?
>>
>
> It's done automatically.  You should see a window pop up indicating
> missing atoms and that they have been built back.  Then just save the .pdb
> file.  There are tutorials online for this and you should consult whatever
> documentation and help forums SwissPDBViewer may provide.
>
>
> -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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Re: [gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

[James Lord]

Hi Justin,
I opened up the strucutre in Swissviewr. Then how can I have a pdb with
missing parts added?
Cheers
James

On Tuesday, May 5, 2015, Justin Lemkul  wrote:

>
>
> On 5/5/15 4:32 AM, James Lord wrote:
>
>> Dear gmx users,
>>
>> pdb2gmx is complaining about Incomplete ring in HIS3, for 3V03.pdb
>>
>> I saw Justin's comment
>> "All structures have to be complete in order for pdb2gmx to process them.
>> The only atoms it can add are hydrogens. All heavy atoms are required. If
>> you place the missing atom(s) correctly, according to proper geometry,
>> you shouldn't
>> be changing the structure too much, but a simple energy minimization after
>> you've generated the topology should relax any poor geometry.
>>
>> Justin"
>>
>> And also Florian comment on this
>>
>> "you should take a look at the structure in your favorite viewer,
>> perhaps some residues are missing and/ or
>> are not resolved completly by Xray/ NMR. Take a look
>> at REMARKS in this pdb file.
>>
>> Programs for modelling missing residues are:
>>
>> Swiss
>>
>> pdb
>> viewer
>>
>> WHATIF
>>
>> pymol
>>
>> vmd
>>
>> or
>>
>> commercial
>> onces:
>>
>> MOE
>>
>> Accelyrs
>>
>> Discovery
>> Studio"
>>
>> I  see following remarks in the .pdb
>>
>> REMARK
>> 465 MISSING RESIDUES
>>
>
> Missing residues are important if they are internal or otherwise important
> for function.  Frequently, terminal residues are disordered and cannot be
> resolved by crystallography.
>
>  REMARK
>> 470 MISSING ATOM
>>
>>
>> REMARK
>> 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
>>
>>
> Here's the most important section of your PDB file (at least, in this
> context):
>
> REMARK 470 MISSING ATOM
> REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
> REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
> REMARK 470 I=INSERTION CODE):
> REMARK 470   M RES CSSEQI  ATOMS
> REMARK 470 HIS A   3CG   ND1  CD2  CE1  NE2
> REMARK 470 LYS A   4CE   NZ
> REMARK 470 LYS A  41CD   CE   NZ
> REMARK 470 LYS A  76CE   NZ
> ...
>
> You have hundreds and hundreds of missing atoms in this structure.  They
> need to be modeled back or there will be no way to produce a topology.
>
>
>> REMARK
>> 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
>>
>>
>> REMARK
>> 470 I=INSERTION CODE):
>>
>> 1-I also looked at the structure in VMD but how can I see the
>> missingatoms/residues?How to know what type of atom/residues are
>> missing? I just can see residue number
>>
>>
> Read the contents of the PDB file, i.e. the snippet that I posted.
>
>  2- How to add them? Again somewhere else Justin is saying “add the missing
>> atoms with emacs (or another text editor). Then minimize” .
>>
>>
> This certainly doesn't apply to you.  If you're missing an atom or two,
> it's trivial to calculate where they should be based on existing atoms.  In
> your case, you have a huge amount of missing atoms.  Try SwissPDBViewer
> (which adds back missing atoms as soon as you open the file - convenient!)
> or anything else you might like (I think WHATIF can do this, too, but I've
> never done 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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] gromacs-5.0.4 installation problem

[James Lord]

YAY :-) it is working, Do not know what was wrong but apparently something
was seriously messed up with cmake and compilers, removed cmake and gcc
gcc++ complier and gromacs, re-doing solved the problem.

*sudo apt-get update -y*
*sudo apt-get update**sudo apt-get install cmake*
Cheers
James

On Thu, May 7, 2015 at 7:45 PM, Roland Schulz  wrote:

> Hi,
>
> please rerun cmake from an empty build directly and post both the full
> cmake output and the content of CMakeFiles/CMakeError.log.
>
> Roland
>
> On Thu, May 7, 2015 at 7:38 PM, James Lord 
> wrote:
>
> > Hi Mark,Szilard and Christopher,
> > Thanks for the comments,
> > apparently gcc 4.8.2 is there. Really can't understand why and what it is
> > complaining about,
> >
> > root@ubuntu:~/gromacs-5.0.4/build# gcc --version
> > gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2
> > Copyright (C) 2013 Free Software Foundation, Inc.
> > This is free software; see the source for copying conditions.  There is
> NO
> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
> >
> >
> > So are you guys saying that a new installation might be better than
> messing
> > around with this?
> > Cheers
> > James
> >
> >
> >
> > On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll 
> > wrote:
> >
> > > Something is strange about that Ubuntu installation, gcc 4.8.2 should
> > > be the default.
> > > --
> > > Szilárd
> > >
> > >
> > > On Fri, May 8, 2015 at 12:10 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > > > Hi,
> > > >
> > > > The error means you need a newer compiler in order to take advantage
> of
> > > > your hardware, e.g. the latest version of gcc you can get (which will
> > > > probably require you add a new PPA), though I am surprised that cmake
> > > found
> > > > a C++ compiler on 14.04 and then didn't find AVX support in it...
> > > something
> > > > seems strange.
> > > >
> > > > Mark
> > > >
> > > > On Thu, May 7, 2015 at 8:46 PM Christopher Neale <
> > > > chris.ne...@alum.utoronto.ca> wrote:
> > > >
> > > >> Gromacs only notified you about turning off the GPU code, that was
> not
> > > an
> > > >> error. The error was the AVX vs. SSE4.1 problem. Not sure why you
> are
> > > >> getting that since I thought cmake would get these things straight.
> > > >>
> > > >> Chris.
> > > >>
> > > >> 
> > > >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > > >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
> James
> > > >> Lord 
> > > >> Sent: 07 May 2015 14:05
> > > >> To: gmx-us...@gromacs.org
> > > >> Subject: [gmx-users] gromacs-5.0.4 installation problem
> > > >>
> > > >> Hi all,
> > > >> I just installed a fresh ubuntu 14.04, and want to go ahead with
> > > >> gromacs-5.0.4 installation, I am constantly getting this annoying
> > > message,
> > > >> anyone can help?
> > > >>
> > > >> root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > > >> -DREGRESSIONTEST_DOWNLOAD=ON
> > > >> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > > >> acceleration
> > > >> CMake Error at cmake/gmxTestSimd.cmake:220 (message):
> > > >>   Cannot find AVX compiler flag.  Use a newer compiler, or choose
> > SSE4.1
> > > >> SIMD
> > > >>   (slower).
> > > >> Call Stack (most recent call first):
> > > >>   CMakeLists.txt:716 (gmx_test_simd)
> > > >>
> > > >>
> > > >> -- Configuring incomplete, errors occurred!
> > > >> See also
> "/home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log".
> > > >> See also
> "/home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log".
> > > >>
> > > >> After this I did
> > > >> sudo apt-get install nvidia-cuda-toolkit
> > > >> but still i am getting the same message
> > > >> Any comments?
> > > >> Cheers
> > > >> James
> > > >> --
> > > >> Gromacs Users mailing list
> > > >>
&g

Re: [gmx-users] gromacs-5.0.4 installation problem

[James Lord]

Hi Mark,Szilard and Christopher,
Thanks for the comments,
apparently gcc 4.8.2 is there. Really can't understand why and what it is
complaining about,

root@ubuntu:~/gromacs-5.0.4/build# gcc --version
gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


So are you guys saying that a new installation might be better than messing
around with this?
Cheers
James



On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll  wrote:

> Something is strange about that Ubuntu installation, gcc 4.8.2 should
> be the default.
> --
> Szilárd
>
>
> On Fri, May 8, 2015 at 12:10 AM, Mark Abraham 
> wrote:
> > Hi,
> >
> > The error means you need a newer compiler in order to take advantage of
> > your hardware, e.g. the latest version of gcc you can get (which will
> > probably require you add a new PPA), though I am surprised that cmake
> found
> > a C++ compiler on 14.04 and then didn't find AVX support in it...
> something
> > seems strange.
> >
> > Mark
> >
> > On Thu, May 7, 2015 at 8:46 PM Christopher Neale <
> > chris.ne...@alum.utoronto.ca> wrote:
> >
> >> Gromacs only notified you about turning off the GPU code, that was not
> an
> >> error. The error was the AVX vs. SSE4.1 problem. Not sure why you are
> >> getting that since I thought cmake would get these things straight.
> >>
> >> Chris.
> >>
> >> 
> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James
> >> Lord 
> >> Sent: 07 May 2015 14:05
> >> To: gmx-us...@gromacs.org
> >> Subject: [gmx-users] gromacs-5.0.4 installation problem
> >>
> >> Hi all,
> >> I just installed a fresh ubuntu 14.04, and want to go ahead with
> >> gromacs-5.0.4 installation, I am constantly getting this annoying
> message,
> >> anyone can help?
> >>
> >> root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON
> >> -DREGRESSIONTEST_DOWNLOAD=ON
> >> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> >> acceleration
> >> CMake Error at cmake/gmxTestSimd.cmake:220 (message):
> >>   Cannot find AVX compiler flag.  Use a newer compiler, or choose SSE4.1
> >> SIMD
> >>   (slower).
> >> Call Stack (most recent call first):
> >>   CMakeLists.txt:716 (gmx_test_simd)
> >>
> >>
> >> -- Configuring incomplete, errors occurred!
> >> See also "/home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log".
> >> See also "/home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log".
> >>
> >> After this I did
> >> sudo apt-get install nvidia-cuda-toolkit
> >> but still i am getting the same message
> >> Any comments?
> >> Cheers
> >> James
> >> --
> >> 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.
> >> --
> >> 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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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
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> posting!
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[gmx-users] gromacs-5.0.4 installation problem

[James Lord]

Hi all,
I just installed a fresh ubuntu 14.04, and want to go ahead with
gromacs-5.0.4 installation, I am constantly getting this annoying message,
anyone can help?

root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU
acceleration
CMake Error at cmake/gmxTestSimd.cmake:220 (message):
  Cannot find AVX compiler flag.  Use a newer compiler, or choose SSE4.1
SIMD
  (slower).
Call Stack (most recent call first):
  CMakeLists.txt:716 (gmx_test_simd)


-- Configuring incomplete, errors occurred!
See also "/home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log".
See also "/home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log".

After this I did
sudo apt-get install nvidia-cuda-toolkit
but still i am getting the same message
Any comments?
Cheers
James
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[gmx-users] Area/enegy at liquid/liquid interface

[James Lord]

Hi all,
How to calculate the area occupied by a protein in atomistic simulation (I
have performed the simulation already) but now want to calculate the area
occupied by the protein at two liquid interfaces and also interfacial free
energy reduction upon adsorption. Any detailed instructions is much
appreciated.
Cheers
James
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[gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

[James Lord]

Dear gmx users,

pdb2gmx is complaining about Incomplete ring in HIS3, for 3V03.pdb

I saw Justin's comment
"All structures have to be complete in order for pdb2gmx to process them.
The only atoms it can add are hydrogens. All heavy atoms are required. If
you place the missing atom(s) correctly, according to proper geometry,
you shouldn't
be changing the structure too much, but a simple energy minimization after
you've generated the topology should relax any poor geometry.

Justin"

And also Florian comment on this

"you should take a look at the structure in your favorite viewer,
perhaps some residues are missing and/ or
are not resolved completly by Xray/ NMR. Take a look
at REMARKS in this pdb file.

Programs for modelling missing residues are:

Swiss

pdb
viewer

WHATIF

pymol

vmd

or

commercial
onces:

MOE

Accelyrs

Discovery
Studio"

I  see following remarks in the .pdb

REMARK
465 MISSING RESIDUES


REMARK
465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE


REMARK
465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN


REMARK
465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)

REMARK
470 MISSING ATOM


REMARK
470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;


REMARK
470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;


REMARK
470 I=INSERTION CODE):

1-I also looked at the structure in VMD but how can I see the
missingatoms/residues?How to know what type of atom/residues are
missing? I just can see residue number

2- How to add them? Again somewhere else Justin is saying “add the missing
atoms with emacs (or another text editor). Then minimize” .

May I ask someone to walk me through these steps?

Cheers

James
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Re: [gmx-users] Justin biphasic tutorial with controlled adsoption of protein

[James Lord]

Hi Justin,
I definitely saw this in the manual but as I said before couldn't get the
part "a suitable [position_restraints] " and "negative force constant" in
your earlier email. Would you please let me know the right way of doing
this? may be an example of the command etc to be used?
Cheers
James

On Mon, May 4, 2015 at 4:28 AM, Justin Lemkul  wrote:

>
>
> On 5/3/15 9:07 AM, James Lord wrote:
>
>> Hi Justin,
>> Thanks for the info, your assumption re long axis of the box is correct
>> (z),
>> here is the .gro file I have for one the oil (decane)-protein (the
>> protein is in
>> the middle part of the free space above the oil surface). Is that what
>> you were
>> talking about? I went through manual and could not get what to do for
>> position
>> restrains, appreciate if you can elaborate further on it? Thanks for your
>> final
>> point re solvent/ions separate coupling.
>>
>
> Restraints require a reference coordinate for each atom to which
> restraints are applied.  Normally this is read from -c when running grompp
> (useful for absolute restraints), but the origin of the restraint can be
> replaced with a reference position in -r.  If you're trying to restrain a
> molecule to some region of space (what you're trying to do here), you
> basically need to define some coordinate along the axis/axes of interest
> that defines a boundary for the potential.  If you're trying to restrict
> motion along z, then the z-coordinates of all the atoms to which restraints
> are applied need to be set to this value.  The coordinate file passed to -r
> is thus not physically the coordinates of the molecule, but defines a
> reference location at which the restraints are applied.  This is also
> useful for doing, e.g. osmotic pressure calculations - you can restrain
> ions within a certain region of space and the waters can move freely; a
> virtual semi-permeable membrane.  Could be a useful toy system for you to
> debug any issues you might run into.
>
>
> -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] Justin biphasic tutorial with controlled adsoption of protein

[James Lord]

Hi Justin,
Thanks for the info, your assumption re long axis of the box is correct
(z), here is the .gro file I have for one the oil (decane)-protein (the
protein is in the middle part of the free space above the oil surface). Is
that what you were talking about? I went through manual and could not get
what to do for position restrains, appreciate if you can elaborate further
on it? Thanks for your final point re solvent/ions separate coupling.
https://drive.google.com/file/d/0B0YMTXH1gmQsYmQzRXUtN1ZENmc/view?usp=sharing
Cheers
James


On Sun, May 3, 2015 at 4:23 AM, Justin Lemkul  wrote:

>
>
> On 5/2/15 10:02 AM, James Lord wrote:
>
>> Dear gmx users,
>> I have a biphasic system, like Justin's tutorial, but I want to control
>> the protein to adsorb/desorb from the oil-water interface, I don't want
>> the
>> protein to go through oil phase just want to keep it at the interface, I
>> have added a constant force at the end of the mdp file. i tried different
>> pull_k1 values but what I see is, when the force is applied the oil is
>> also
>> deformed (which makes sense) and kinda make a hole in the oil phase and
>> eventually pass through it. I just want to keep it at or away from the
>> interface without deforming/puling away the oil molecules, What is the
>> best
>> way to do it? any suggestion? here is the mdp
>> https://drive.google.com/open?id=0B0YMTXH1gmQsZ1ljOUZROWNGM3M&authuser=0
>>
>>
> I wouldn't use the pull code.  This sounds like a task best suited for a
> flat-bottom restraint.  I'm going to assume the long axis of the box is
> along z for this example. You can create a coordinate file in which the
> z-coordinate of all the protein atoms is equal to the middle of the box
> (this assumes the z dimension of the box doesn't change, e.g. semiisotropic
> pressure coupling with compressibility of zero along z).  Then supply this
> file to grompp -r with a suitable [position_restraints] section that
> specifies a flat-bottom potential along z (see manual section 4.3.2, I
> think this is a case where you need a negative force constant to keep the
> atoms "outside" of the restraint region). During the run, if any protein
> atom hits the imaginary wall, it gets pushed back in the other direction by
> the flat-bottom restraint.
>
> Also, don't couple solvent and ions to separate thermostats.  It's not
> sensible and usually not stable.
>
> -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] Justin biphasic tutorial with controlled adsoption of protein

[James Lord]

Dear gmx users,
I have a biphasic system, like Justin's tutorial, but I want to control
the protein to adsorb/desorb from the oil-water interface, I don't want the
protein to go through oil phase just want to keep it at the interface, I
have added a constant force at the end of the mdp file. i tried different
pull_k1 values but what I see is, when the force is applied the oil is also
deformed (which makes sense) and kinda make a hole in the oil phase and
eventually pass through it. I just want to keep it at or away from the
interface without deforming/puling away the oil molecules, What is the best
way to do it? any suggestion? here is the mdp
https://drive.google.com/open?id=0B0YMTXH1gmQsZ1ljOUZROWNGM3M&authuser=0

cheers
James
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Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories

[James Lord]

Hi Mahboobeh,
I recommend checking the created trajectories with gmx check.
Cheers
James

On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang  wrote:

> Hi，-e is end frame， -b is the start one.
>
> Sent from my Huawei Mobile
>
> Mahboobeh Eslami  wrote:
>
> hi GMx user I simulated protein-ligand comolex with gromacs. total
> simulation time is 20ns. when I use trjconv for cutting the  trajectory
> in  small   subtrajectories from 1ps to 17000ps by following command:
> trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000
> I see following text in terminal window;
> Reading frame   0 time 1.000
> Precision of md-nopbc.xtc is 0.001 (nm)
> Using output precision of 0.001 (nm)
>  ->  frame   3500 time 17000.000->  frame   3000 time 16000.000
> I think the generated trajectory is incomplete because saved frame is
> incomplete. please guide me.
> Many thanks tobest
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Re: [gmx-users] Forced adsoprtion and desorption of a protein on a surface

[James Lord]

Thanks heaps mastermind Justin.
James

On Thursday, April 9, 2015, Justin Lemkul  wrote:

>
>
> On 4/9/15 2:45 AM, James Lord wrote:
>
>> Dear Users,
>> I am wondering if anyone can help me out with forced adsorption/
>> desorption
>> of a protein on surface. I am aware of pulling code in Justin's tutorial
>> but that is not what I am looking for. I want a simple constant force
>> (perpendicular to the surface) method to push and/or pull the protein
>> (center of mass) onto /or from a surface at specific time intervals during
>> the simulation . Appreciate any comments.
>>
>
> There's no way to tell mdrun to apply the pull code only during given time
> intervals, so you'd have to run for some time, create a new .tpr that
> contains pulling instructions to continue while applying the biasing
> potential, turn off the pull code or change it, repeat as needed.
>
> -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] Forced adsoprtion and desorption of a protein on a surface

[James Lord]

Dear Users,
I am wondering if anyone can help me out with forced adsorption/ desorption
of a protein on surface. I am aware of pulling code in Justin's tutorial
but that is not what I am looking for. I want a simple constant force
(perpendicular to the surface) method to push and/or pull the protein
(center of mass) onto /or from a surface at specific time intervals during
the simulation . Appreciate any comments.
Cheers
James
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Re: [gmx-users] Distance of residue’s centre of mass to a surface (COM)

[James Lord]

Hi Justin,
Thanks,
g_dist is calculating the centre of mass of two groups and -dist option
print all atoms in group 2 closer than dist to
the centre of mass of group 1, while what I am looking after is the
distance of COM of residues to a surface not the centre of mass of the
surface. Am I missing anything?
Cheers
James


On Sat, Mar 28, 2015 at 1:17 AM, Justin Lemkul  wrote:

>
>
> On 3/27/15 8:03 AM, James Lord wrote:
>
>> Dear users,
>> If I want to calculate distance of each residue's COM of a protein to a
>> surface is g_mindist going to be my friend? It is documented that
>> "g_mindist computes the distance between one group and a number of other
>> groups. Both the minimum distance and the number of contacts within a
>> given
>> distance are written to two separate output files".
>>
>
> Use g_dist, not g_mindist.
>
> -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] Distance of residue’s centre of mass to a surface (COM)

[James Lord]

Dear users,
If I want to calculate distance of each residue's COM of a protein to a
surface is g_mindist going to be my friend? It is documented that
"g_mindist computes the distance between one group and a number of other
groups. Both the minimum distance and the number of contacts within a given
distance are written to two separate output files".
Cheers
James
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[gmx-users] g_mindist

[James Lord]

Dear users,
I have MD of protein adsorption at an oil phase and am trying to calculate
the number of residues that contact the oil at each point in time? I have
tried
g_mindist -f mol.xtc -s md.tpr -on  numcont.xvg
also with -group option but none of them gave what I am looking for. any
comments??
Cheers
James
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[gmx-users] Protein distance with respect to box walls

[James Lord]

Dear Users,
I have a protein in a box and was wondering to know how to figure out the
protein distance to the box walls? I can see the box dimensions at the end
of .gro file but how to know what is (x,y,z) of protein in the box?? any
comments?
Cheers
James
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[gmx-users] How to obtaine different protein orientations in a biphasic system

[James Lord]

Dear users,
I have inserted a protein in a biphasic system (like Justin tutorial). My
question is if I want to sample different orientations of protein to one of
the phases how should I do that? I have rotated the protein with different
angles  (90,180,270) around X,Y,Z axes  but as I have periodic boundary
condition in XYZ, Am I really obtaining different orientations? any
comments is appreciated
Cheers
James
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Hi Justin,
Would you please tell me from the files I sent you which of them you
checked and how you got to the conclusion that  (I mean which command )
"This system behaves correctly - there is a zero interaction energy (both
Coulomb and LJ) at t=0, so it is fine".
Thanks
James

On Mon, Oct 20, 2014 at 3:26 AM, Justin Lemkul  wrote:

>
>
> On 10/19/14 7:26 AM, James Lord wrote:
>
>> Hi Justin,
>> Well, I tried clicking three different things that said download, but
>> every
>> one of them tried to download software, spam, or charge me money, so I'm
>> going to assume that the files you sent me off-list are the same ones
>> you've posted here.  If that's not the case, please find a better place to
>> share files.  Google Docs works well.
>> Thanks Google Docs  will be used for future.
>>
>> How many different systems do you have?  You said before you had an
>> all-atom surface of polyethylene.  This system is a united-atom layer of
>> decane.
>>
>> I have protein at different liquid-solid interfaces, and I want to have
>> interaction energy of all of them.  I think I explained to you in the
>> email
>> with attachment why I am sending this (as I have done so many changes to
>> protein-PE that I lost track of them)
>>
>>
> Well you now have a reference for what "should" work, so hopefully that is
> helpful.  If the PE system is giving issues, please provide *those* files
> so they can be diagnosed and you can get a solution.  If you're having
> trouble keeping track of your own work, it's fairly helpless for anyone
> else to try ;)
>
>
> -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 to calculate protein-surface interaction energy

[James Lord]

Hi Justin,
Well, I tried clicking three different things that said download, but every
one of them tried to download software, spam, or charge me money, so I'm
going to assume that the files you sent me off-list are the same ones
you've posted here.  If that's not the case, please find a better place to
share files.  Google Docs works well.
Thanks Google Docs  will be used for future.

How many different systems do you have?  You said before you had an
all-atom surface of polyethylene.  This system is a united-atom layer of
decane.

I have protein at different liquid-solid interfaces, and I want to have
interaction energy of all of them.  I think I explained to you in the email
with attachment why I am sending this (as I have done so many changes to
protein-PE that I lost track of them)

If you want people to spend time helping you, you need to provide accurate
information.  This system behaves correctly - there is a zero interaction
energy (both Coulomb and LJ) at t=0, so it is fine.

If it is correct (which when I plot the energy it is not) then I will
correct the protein-PE ones.

But I don't know what I'm supposed to be spending my time doing, because
this isn't the system you described before as being problematic.
Cheers
James

-Justin

On Sun, Oct 19, 2014 at 4:18 PM, Justin Lemkul  wrote:

>
>
> On 10/18/14 10:41 PM, James Lord wrote:
>
>> Hi Justin,
>> Here is the uploaded files on 4share.
>> http://www.4shared.com/folder/9CgRBgqp/_online.html
>>
>
> Well, I tried clicking three different things that said download, but
> every one of them tried to download software, spam, or charge me money, so
> I'm going to assume that the files you sent me off-list are the same ones
> you've posted here.  If that's not the case, please find a better place to
> share files.  Google Docs works well.
>
> How many different systems do you have?  You said before you had an
> all-atom surface of polyethylene.  This system is a united-atom layer of
> decane.  If you want people to spend time helping you, you need to provide
> accurate information.  This system behaves correctly - there is a zero
> interaction energy (both Coulomb and LJ) at t=0, so it is fine.  But I
> don't know what I'm supposed to be spending my time doing, because this
> isn't the system you described before as being problematic.
>
> -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 to calculate protein-surface interaction energy

[James Lord]

Hi Justin,
Here is the uploaded files on 4share.
http://www.4shared.com/folder/9CgRBgqp/_online.html
Cheers
James

On Sun, Oct 19, 2014 at 2:23 PM, James Lord 
wrote:

> Hi Diogo,
> Yes that is what I have at the end of top file.
> ps: Sorry Justin I just saw your previous email.
> Cheers
> James
>
> On Sun, Oct 19, 2014 at 2:13 PM, Diogo Martins de Sá 
> wrote:
>
>> At the end of your topology file, what molecules do you have written
>> down?
>> You should have something like:
>> Protein
>> Surface
>> SOL
>> Ion (if you needed to equilibrate system)
>>
>>
>> Diogo
>>
>>
>>
>>
>> --
>>  Date: Thu, 16 Oct 2014 12:07:15 -0400
>>  From: Justin Lemkul 
>>  To: gmx-us...@gromacs.org
>>  Subject: Re: [gmx-users] How to calculate protein-surface interaction
>>  energy
>>  Message-ID: <543fed33.5010...@vt.edu>
>>  Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>>  On 10/16/14 11:42 AM, James Lord wrote:
>>  > Hi Justin,
>>  > Sorry for not being clear, I have done the simulation without
>> specifying
>>  > the energygrps, so based on your previous comment I should use mdrun
>> -rerun
>>  > trj.xtc -o energy.edr -pn index.ndx? and in index file define
>> energygrps =
>>  > Protein Surface right?
>>  >
>>  > If not appreciate if you give an example of the command with
>> appropriate
>>  > input output etc.
>>
>>  Create a new .tpr with the .mdp file that specifies the desired
>> energygrps, then:
>>
>>  mdrun -s new.tpr -rerun trj.xtc
>>
>>  -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
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Hi Diogo,
Yes that is what I have at the end of top file.
ps: Sorry Justin I just saw your previous email.
Cheers
James

On Sun, Oct 19, 2014 at 2:13 PM, Diogo Martins de Sá 
wrote:

> At the end of your topology file, what molecules do you have written
> down?
> You should have something like:
> Protein
> Surface
> SOL
> Ion (if you needed to equilibrate system)
>
>
> Diogo
>
>
>
>
> --
>  Date: Thu, 16 Oct 2014 12:07:15 -0400
>  From: Justin Lemkul 
>  To: gmx-us...@gromacs.org
>  Subject: Re: [gmx-users] How to calculate protein-surface interaction
>  energy
>  Message-ID: <543fed33.5010...@vt.edu>
>  Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
>  On 10/16/14 11:42 AM, James Lord wrote:
>  > Hi Justin,
>  > Sorry for not being clear, I have done the simulation without
> specifying
>  > the energygrps, so based on your previous comment I should use mdrun
> -rerun
>  > trj.xtc -o energy.edr -pn index.ndx? and in index file define
> energygrps =
>  > Protein Surface right?
>  >
>  > If not appreciate if you give an example of the command with
> appropriate
>  > input output etc.
>
>  Create a new .tpr with the .mdp file that specifies the desired
> energygrps, then:
>
>  mdrun -s new.tpr -rerun trj.xtc
>
>  -Justin
>
>  --
>  ==
>
>  Justin A. Lemkul, Ph.D.
>  Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>  Department of Pharmaceutical Sciences
>  School of Pharmacy
>  Health Sciences Facility II, Room 629
>  University of Maryland, Baltimore
>  20 Penn St.
>  Baltimore, MD 21201
>
>  jalem...@outerbanks.umaryland.edu | (410) 706-7441
>  http://mackerell.umaryland.edu/~jalemkul
>
>  =
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Hi Justin,
Thanks, apparently I am doing some silly mistakes as I checked for another
system I have and ended up to the same problem. I am sending all the files
to your personal email and then if the problem is solved I will send a post
with description of the problem and the solution to the mailing list. Is
that fine with you?
Cheers
James

On Sun, Oct 19, 2014 at 4:26 AM, Justin Lemkul  wrote:

>
>
> On 10/18/14 9:55 AM, James Lord wrote:
>
>> You are right it is the name of molecule type in .top, and thus no error
>> upon executing grompp, so index group is constructed correctly right???
>>
>
> In theory, but if you're saying that at t=0, LJ-SR is not zero, something
> is weird.  Without access to your files, it's impossible to diagnose that
> any further.
>
> -Justin
>
>
>  rvdw=1 nm so should be fine. and for the last part I agree.
>> Cheers
>> James
>>
>> On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 10/18/14 9:30 AM, James Lord wrote:
>>>
>>>  Hi Justin,
>>>>
>>>> 1. Make sure your index groups are correctly constructed.
>>>> Do I need to use make ndx? I thought just adding energygrps=protein
>>>> surface
>>>> at the end of .mdp is enough?
>>>>
>>>>
>>>>  "Surface" isn't likely a default group (unless that's the name of the
>>> [moleculetype]) and grompp should have raised a fatal error if the group
>>> wasn't defined.
>>>
>>>   2. What does 5 nm correspond to?  A COM distance?  A minimum
>>> distance?  If
>>>
>>>> the latter, then the LJ-SR energy should likely be zero, but if it's a
>>>> COM
>>>> distance, that's not necessarily the case.
>>>> 5 nm is minimum distance
>>>>
>>>>
>>>>  OK, in this case, the initial LJ-SR should be zero, provided that rvdw
>>> < 5.
>>>
>>>   3. Is your PE model united-atom or all-atom?  If the latter, you still
>>>
>>>> have
>>>> partial charges that will contribute to a negative Coul-SR (of course,
>>>> this
>>>> is something you can check very simply
>>>> It is all atom
>>>>
>>>>
>>> Then you must have partial charges on the individual atoms and therefore
>>> Coul-SR will be non-zero.
>>>
>>>
>>> -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.
>>>
>>>
> --
> ==
>
> 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/
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

You are right it is the name of molecule type in .top, and thus no error
upon executing grompp, so index group is constructed correctly right???
rvdw=1 nm so should be fine. and for the last part I agree.
Cheers
James

On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul  wrote:

>
>
> On 10/18/14 9:30 AM, James Lord wrote:
>
>> Hi Justin,
>>
>> 1. Make sure your index groups are correctly constructed.
>> Do I need to use make ndx? I thought just adding energygrps=protein
>> surface
>> at the end of .mdp is enough?
>>
>>
> "Surface" isn't likely a default group (unless that's the name of the
> [moleculetype]) and grompp should have raised a fatal error if the group
> wasn't defined.
>
>  2. What does 5 nm correspond to?  A COM distance?  A minimum distance?  If
>> the latter, then the LJ-SR energy should likely be zero, but if it's a COM
>> distance, that's not necessarily the case.
>> 5 nm is minimum distance
>>
>>
> OK, in this case, the initial LJ-SR should be zero, provided that rvdw < 5.
>
>  3. Is your PE model united-atom or all-atom?  If the latter, you still
>> have
>> partial charges that will contribute to a negative Coul-SR (of course,
>> this
>> is something you can check very simply
>> It is all atom
>>
>
> Then you must have partial charges on the individual atoms and therefore
> Coul-SR will be non-zero.
>
>
> -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
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Hi Justin,

1. Make sure your index groups are correctly constructed.
Do I need to use make ndx? I thought just adding energygrps=protein surface
at the end of .mdp is enough?

2. What does 5 nm correspond to?  A COM distance?  A minimum distance?  If
the latter, then the LJ-SR energy should likely be zero, but if it's a COM
distance, that's not necessarily the case.
5 nm is minimum distance

3. Is your PE model united-atom or all-atom?  If the latter, you still have
partial charges that will contribute to a negative Coul-SR (of course, this
is something you can check very simply
It is all atom
Cheers
James

On Sun, Oct 19, 2014 at 2:05 AM, Justin Lemkul  wrote:

>
>
> On 10/18/14 8:51 AM, James Lord wrote:
>
>> Hi Justin,
>> Thanks for the prompt answer. I selected LJ-(SR) but I am getting a
>> positive fluctuating line over the simulation time. Looking at the vmd
>> movie I can see that protein (Lysozyme) is coming into contact with
>> surface
>> afte 10ns and is 5 nm away at the beginning?? my surface is a not charged
>> (polyethylene)?? I'd expect zero energy at beginning and upon touching the
>> surface negative value??? any comments? Sorry this has nothing to do with
>> Gromacs.
>>
>
> A few things:
>
> 1. Make sure your index groups are correctly constructed.
> 2. What does 5 nm correspond to?  A COM distance?  A minimum distance?  If
> the latter, then the LJ-SR energy should likely be zero, but if it's a COM
> distance, that's not necessarily the case.
> 3. Is your PE model united-atom or all-atom?  If the latter, you still
> have partial charges that will contribute to a negative Coul-SR (of course,
> this is something you can check very simply)
>
>
> -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
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Hi Justin,
Thanks for the prompt answer. I selected LJ-(SR) but I am getting a
positive fluctuating line over the simulation time. Looking at the vmd
movie I can see that protein (Lysozyme) is coming into contact with surface
afte 10ns and is 5 nm away at the beginning?? my surface is a not charged
(polyethylene)?? I'd expect zero energy at beginning and upon touching the
surface negative value??? any comments? Sorry this has nothing to do with
Gromacs.
Cheers
James


On Sat, Oct 18, 2014 at 11:48 PM, Justin Lemkul  wrote:

>
>
> On 10/18/14 6:45 AM, James Lord wrote:
>
>> Dear Justin & Diogo,
>> Thanks for your comments, I did the steps you guys mentioned to calculate
>> protein-suface interaction energy and expect to see "protein surface"
>> option upon running g_energy but it is not the case, any comments? Here is
>> what I did,
>> gedit md.mdp and then added at the end of md.mdp file
>> energygrps= protein surface
>> saved it and
>> grompp -f md.mdp -c  mdw.gro -t mdw.cpt -p toplgy.top -o mdnew
>> mdrun -s mdnew.tpr -rerun mdw.xtc
>>
>> g_energy -f mdnew.edr -o energy.xvg
>>
>>
> You will not see a single energy term; rather you will see both LJ and
> Coulombic terms like LJ-SR(Protein:Surface).
>
> -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
>
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Dear Justin & Diogo,
Thanks for your comments, I did the steps you guys mentioned to calculate
protein-suface interaction energy and expect to see "protein surface"
option upon running g_energy but it is not the case, any comments? Here is
what I did,
gedit md.mdp and then added at the end of md.mdp file
energygrps= protein surface
saved it and
grompp -f md.mdp -c  mdw.gro -t mdw.cpt -p toplgy.top -o mdnew
mdrun -s mdnew.tpr -rerun mdw.xtc

g_energy -f mdnew.edr -o energy.xvg

Thanks
James

On Sat, Oct 18, 2014 at 8:52 AM, Diogo Martins de Sá 
wrote:

> open your .mdp in an editor and under energygrps, add " ProteinSurface"
> after the last term.
> Run grompp using this .mdp and create a new .tpr. Then use the command
> line Justin mentioned last.
>
>
> Diogo
>
>
>
>
> --
>  Date: Thu, 16 Oct 2014 12:07:15 -0400
>  From: Justin Lemkul 
>  To: gmx-us...@gromacs.org
>  Subject: Re: [gmx-users] How to calculate protein-surface interaction
>  energy
>  Message-ID: <543fed33.5010...@vt.edu>
>  Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
>  On 10/16/14 11:42 AM, James Lord wrote:
>  > Hi Justin,
>  > Sorry for not being clear, I have done the simulation without
> specifying
>  > the energygrps, so based on your previous comment I should use mdrun
> -rerun
>  > trj.xtc -o energy.edr -pn index.ndx? and in index file define
> energygrps =
>  > Protein Surface right?
>  >
>  > If not appreciate if you give an example of the command with
> appropriate
>  > input output etc.
>
>  Create a new .tpr with the .mdp file that specifies the desired
> energygrps, then:
>
>  mdrun -s new.tpr -rerun trj.xtc
>
>  -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
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Hi Justin,
Sorry for not being clear, I have done the simulation without specifying
the energygrps, so based on your previous comment I should use mdrun -rerun
trj.xtc -o energy.edr -pn index.ndx?  and in index file define energygrps =
Protein Surface right?

If not appreciate if you give an example of the command with appropriate
input output etc.
Cheers
James

On Fri, Oct 17, 2014 at 3:49 AM, Justin Lemkul  wrote:

>
>
> On 10/16/14 10:47 AM, James Lord wrote:
>
>> Hi Justin,
>> Thanks, the .mdp is the same as your tutorial for lysozyme, Can you
>> explain
>> a bit more what to do? if I want to have total energy= vdw and
>> electrostatic?
>>
>
> energygrps = Protein Surface
>
> or whatever the names should be.
>
>
> -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
>
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>
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Re: [gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Hi Justin,
Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain
a bit more what to do? if I want to have total energy= vdw and
electrostatic?
Cheers
James



On Fri, Oct 17, 2014 at 12:51 AM, Justin Lemkul  wrote:

>
>
> On 10/16/14 5:46 AM, James Lord wrote:
>
>> Dear users,
>> I want to calculate the interaction energy (energy versus time) of a
>> protein (Lysozyme) adsorption process (20ns) on to a solid surface
>> (polyethylene).
>> when I use gmx energy -f md.edr -o energy.xvg and then selecting total
>> energy I end up with a messy graph!!! I am doing some wrong? secondly, Is
>> there any way to average the energy over the last 10ns of MD trajectory in
>> Gromacs??
>>
>
> Total energy is just as it says, the total energy of the system.  If you
> want to measure interaction energies, you need to make use of energygrps in
> the .mdp file to decompose (short-range) nonbonded energies.  Note that the
> mesh term from PME is not decomposable in any straightforward way.  If you
> did not use energygrps in the .mdp file for the run, create a new .tpr file
> and recalculate the energies in the existing trajectory with mdrun -rerun.
>
> -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] Fwd: How to calculate protein-surface interaction energy

[James Lord]

Dear users,
I want to calculate the interaction energy (energy versus time) of a
protein (Lysozyme) adsorption process (20ns) on to a solid surface
(polyethylene).
when I use gmx energy -f md20ns.edr -o energy.xvg and then selecting total
energy I end up with a messy graph!!! Am I doing some thing wrong?
secondly, Is there any way to average the energy over the last 10ns of MD
trajectory in Gromacs??
Cheers
James
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[gmx-users] Fwd: How to calculate protein-surface interaction energy

[James Lord]

Dear users,
I want to calculate the interaction energy (energy versus time) of a
protein (Lysozyme) adsorption process (20ns) on to a solid surface
(polyethylene).
when I use gmx energy -f md.edr -o energy.xvg and then selecting total
energy I end up with a messy graph!!! I am doing some wrong? secondly, Is
there any way to average the energy over the last 10ns of MD trajectory in
Gromacs??
Cheers
James
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[gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Dear users,
I want to calculate the interaction energy (energy versus time) of a
protein (Lysozyme) adsorption process (20ns) on to a solid surface
(polyethylene).
when I use gmx energy -f md.edr -o energy.xvg and then selecting total
energy I end up with a messy graph!!! I am doing some wrong? secondly, Is
there any way to average the energy over the last 10ns of MD trajectory in
Gromacs??
Cheers
James
-- 
Gromacs Users mailing list

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