Re: [gmx-users] Re: Energy minimization has stopped....

[Justin Lemkul]

On 11/5/13 7:19 AM, Kalyanashis wrote:

I have given my .mdp file,
; title =  trp_drg
warning =  10
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002 ; ps !
nsteps  =  100 ; total 2000.0 ps.
nstcomm =  100
nstxout =  250 ; ouput coordinates every 0.5 ps
nstvout =  1000 ; output velocities every 2.0 ps
nstfout =  0
nstlog  =  100
nstenergy   =  100
nstlist =  100
ns_type =  grid
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdwtype =  cut-off
rvdw=  1.0
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes
; Berendsen temparature coupling is on
Tcoupl  =  berendsen
tau_t   =  1.01.0-0.1  1.0   1.0
tc_grps =  SOLNA protein   OMP   CL
ref_t   =  300300300   300   300


These settings make no sense.  Please read 
http://www.gromacs.org/Documentation/Terminology/Thermostats.



; Pressure coupling is on
pcoupl  =  berendsen ; Use Parrinello-Rahman for research work
pcoupltype  =  isotropic ; Use semiisotropic when working with
membranes
tau_p   =  2.0
compressibility =  4.5e-5
ref_p   =  1.0
refcoord-scaling=  all
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529


And It is a large protein system containing drug molecule and the atoms of
whole system is near about 16000.
As I did not get any .gro file, thus the MD run was not properly finished.
Please suggest me the probable source this kind error.


The run crashes because your energy minimization effectively failed.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Fw: energy minimization problem

[Justin Lemkul]

On 11/4/13 3:29 AM, kiana moghaddam wrote:

Dear Justin

Further to your previous email, I want to calculate free energy for DNA-ligand 
interaction. According to your answer, for more sensitive calculations like 
free energy simulations and normal modes, emtol should be lower than 1. As I 
understand, you mean that for these systems emtol should be 0 or negative. Is 
it really true?



I answered this yesterday:

http://lists.gromacs.org/pipermail/gmx-users/2013-November/085136.html

-Justin

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==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Fw: energy minimization problem

[kiana moghaddam]

Dear Justin

It is obvious that emtol value can not be zero or negative. but you wrote in 
your email  For more sensitive calculations like free energy simulations and 
normal modes, you will want to minimize much more thoroughly (for NM, emtol  
1) and in double precision. what did you mean by saying emtol1? Anyway, my 
question was: for free energy calculation in double precision, what should be 
the best value for emtol? 

Best Regards
Kiana  



On Monday, November 4, 2013 3:40 PM, Justin Lemkul jalem...@vt.edu wrote:
 


On 11/4/13 3:29 AM, kiana moghaddam wrote:
 Dear Justin

 Further to your previous email, I want to calculate free energy for DNA-ligand
 interaction. According to your answer, for more sensitive calculations like 
free energy simulations and normal modes, emtol should be lower than 1. As I 
understand, you mean that for these systems emtol should be 0 or negative. Is 
it really true?


I answered this yesterday:

http://lists.gromacs.org/pipermail/gmx-users/2013-November/085136.html


-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health
 Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441


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Re: [gmx-users] Fw: energy minimization problem

[Justin Lemkul]

On 11/4/13 8:55 AM, kiana moghaddam wrote:

Dear Justin

It is obvious that emtol value can not be zero or negative. but you wrote in
your email  For more sensitive calculations like free energy simulations and
normal modes, you will want to minimize much more thoroughly (for NM, emtol 
1) and in double precision. what did you mean by saying emtol1? Anyway, my


I mean exactly what I said.  You should set emtol to some value of 1 or less as 
a target for NMA.



question was: for free energy calculation in double precision, what should be
the best value for emtol?



I have not worked with systems that have required such strenuous minimization, 
but I believe the general recommendation (if necessary for whatever you're 
working with, and I'm not prepared to try to guess about what you're doing) is 
to minimize as far as you possibly can.  Set some very low value of emtol and 
some very high value of nsteps and let the EM algorithms churn away.  You will 
usually need several rounds of EM using different methods to achieve this. 
Published literature and previous posts to this list (in the archive) should be 
sufficient to guide you.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] RE: Energy Minimization/ NpT settling problem

[Justin Lemkul]

On 12/21/12 2:57 PM, emmanuelle wrote:

Thanks for your reply.

1.My cutoffs are OK. Indeed, changing them leads to the same problem.


This outcome points to a topology or configuration issue.


2.My original box is 20nm in length. I generate it using genconf to avoid
any lack of memory that genbox could provide for a system of such a size.
Then I use editconf to reach the required density of 1000g/l.


Scaling with editconf can shorten or elongate bonds and has never been a very 
robust approach in my hands.  It is better to generate a box that has a 
reasonable density and use sufficient equilibration to achieve the target value 
(within the accuracy of the force field being used).



2b.Atom 13090 is a H atom of an MEA molecule (HO-CH2-CH2-NH2). More
specifically, it is the hydrogen directly bonded to the oxygen.

Surprisingly, when I simulate a similar system for which I only substitute
the monoethanolamine molecules by ethanolamine molecules, everything works
perfectly fine.

Could you help me on this?



Probably the editconf scaling adjusted the coordinates in a bad way.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

[Justin A. Lemkul]

On 6/12/12 12:09 PM, Erica Hicks wrote:

Hi,

I am still working on this error but found that a possible error could be the 
way editconf was used to convert .pdb to .gro in Step 3. I used the command:

editconf -f dppc128.pdb -o dppc128.gro

Is this correct? Would it have been better to use pdb2gmx, instead? ( pdb2gmx 
–f input.pdb –o output.gro -o protein.top –inter ) Why use editconf?



Because all that's needed here is a file format conversion.  Parameters for DPPC 
are not present in most force field .rtp files, so pdb2gmx will throw a fatal 
error.  The job of pdb2gmx is to write a topology; outputting a coordinate file 
is more or less a side effect.  Since we already have a topology for DPPC, and 
the coordinate file matches but simply needs to be in a different format, 
editconf is the easiest solution.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: Energy Minimization - not getting correct lipid area

[Justin A. Lemkul]

On 6/8/12 4:57 PM, Erica Hicks wrote:

It was after just one iteration. The number of lipids removed after scaling
the lipids by a factor of 4 was two. I am not sure how to update this as the
[molecules] directive in the topology.top shows only the number of moles,
i.e. 1.



The number shown in [molecules] is the number of molecules of a given species. 
If you started with 128 lipids, a removal of 4 means you need to list 124 lipids.


I don't know how you can get such a small area with only one iteration of 
shrinking.  Your box should be enormous at that point.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

[Justin A. Lemkul]

On 6/8/12 5:32 PM, Erica Hicks wrote:

Hi,

I went back and found that a possible error could be that the coordinate file 
was not updated correctly. After concatenated the Kalp_newbox.gro and 
dppc128_whole.gro, it said to update the coordinate file with the correct 
number of atoms. This should be the topology.top, right? But when I look 
through this, all I find is:
[ molecules ]
; Compound#mols
Protein 1
Where should the number of atoms be and is topology.top the correct file?


Make sure you added the correct topology information (step 2 in the tutorial, 
note the green text):


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html

Step 3.2 tells you:

Remove unnecessary lines (the box vectors from the KALP structure, the header 
information from the DPPC structure) and update the second line of the 
coordinate file (total number of atoms) accordingly.


The tutorial assumes you're familiar with such operations, so in reality what 
it's implying is that, since you've now concatenated a protein and a 128-lipid 
membrane, you need to add:


DPPC 128

to the [molecules] directive (after the Protein line to keep the correct order). 
 Further manual modifications are necessary based on how many lipids InflateGRO 
removes.


-Justin



Erica

From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998239...@n6.nabble.com]
Sent: Friday, June 08, 2012 4:02 PM
To: Hicks, Erica
Subject: Re: Energy Minimization - not getting correct lipid area



On 6/8/12 4:57 PM, Erica Hicks wrote:

It was after just one iteration. The number of lipids removed after scaling
the lipids by a factor of 4 was two. I am not sure how to update this as the
[molecules] directive in the topology.top shows only the number of moles,
i.e. 1.



The number shown in [molecules] is the number of molecules of a given species.
If you started with 128 lipids, a removal of 4 means you need to list 124 
lipids.

I don't know how you can get such a small area with only one iteration of
shrinking.  Your box should be enormous at that point.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

[Justin A. Lemkul]

On 6/8/12 6:18 PM, Erica Hicks wrote:

Hi,

Everything should be updated correctly. I added in the DPPC 128 underneath
the protein in [molecules] but I still get the same results. What do you mean
by  Further manual modifications are necessary based on how many lipids
InflateGRO removes? After I generated the new position restrain file, I
updated the minim.mdp withe the correct info. I then scaled by a factor of 4,
updated [molecules], ran energy minimization (mdrun -v -deffnm em), and


This is all my comment meant.  If InflateGRO removes 4 lipids, then you have 124 
left, which it sounds like you have accounted for.



scaled by a factor 0.95. I have no idea what could possibly going wrong.
Maybe something with the manipulation of InflateGRO


Please provide the entire screen output of the first shrinking step that 
InflateGRO produces.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

[Justin A. Lemkul]

On 6/8/12 6:33 PM, Erica Hicks wrote:

Hi,

bash-3.2$ perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
Reading.
Scaling lipids
There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...

Writing scaled bilayer  centered protein...


Calculating Area per lipid...
Protein X-min/max: 2640
Protein Y-min/max: 2539
X-range: 14 AY-range: 14 A
Building 14 X 14 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 2 nm^2
Area per lipid: 10.4716089904762 nm^2

Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 10.475577244 nm^2

Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 10.4716089904762 nm^2

Writing Area per lipid...
Done!

bash-3.2$ mdrun -v -deffnm em
Back Off! I just backed up em.log to ./#em.log.6#
Getting Loaded...
Reading file em.tpr, VERSION 4.5.4 (single precision)
Starting 4 threads
Loaded with Money

Making 1D domain decomposition 4 x 1 x 1

Back Off! I just backed up em.trr to ./#em.trr.6#

Back Off! I just backed up em.edr to ./#em.edr.6#

Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot= -3.06212e+05 Fmax= 5.37269e+03, atom= 3275
Step=1, Dmax= 1.0e-02 nm, Epot= -3.10498e+05 Fmax= 2.40668e+03, atom= 3024
Step=3, Dmax= 6.0e-03 nm, Epot= -3.10958e+05 Fmax= 2.89119e+03, atom= 4225
Step=5, Dmax= 3.6e-03 nm, Epot= -3.12589e+05 Fmax= 1.46767e+03, atom= 1365
Step=6, Dmax= 4.3e-03 nm, Epot= -3.13033e+05 Fmax= 3.83969e+03, atom= 1365
Step=7, Dmax= 5.2e-03 nm, Epot= -3.13599e+05 Fmax= 2.88720e+03, atom= 1365
Step=8, Dmax= 6.2e-03 nm, Epot= -3.13688e+05 Fmax= 4.93154e+03, atom= 1365
Step=9, Dmax= 7.5e-03 nm, Epot= -3.14101e+05 Fmax= 4.72541e+03, atom= 1365
Step=   11, Dmax= 4.5e-03 nm, Epot= -3.14800e+05 Fmax= 9.90227e+02, atom= 1365

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.6#

Steepest Descents converged to Fmax  1000 in 12 steps
Potential Energy  = -3.1480012e+05
Maximum force =  9.9022711e+02 on atom 1365
Norm of force =  1.2180042e+02


bash-3.2$ perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 
area_shrink1.dat
Reading.
Scaling lipids
There are 128 lipids...


Something is wrong here.  You should only have 126 lipids since 2 were removed 
before.  Did you minimize the correct coordinate file?



with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

No protein coordinates found...


This is also strange.  This, coupled with the lines above regarding the number 
of lipids, suggest you're using the wrong coordinate file.



Writing scaled bilayer  centered protein...


Calculating Area per lipid...
Protein X-min/max: 1-
Protein Y-min/max: 1-
X-range: -1 AY-range: -1 A
Building -1 X -1 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD..
lower TMD..


The following areas are meaningless, for reasons associated with incorrect 
content or processing thereof.



Area per protein: 0 nm^2
Area per lipid: 0.583197761890625 nm^2

Area per protein, upper half: 0 nm^2
Area per lipid, upper leaflet : 0.583197761890625 nm^2

Area per protein, lower half: 0 nm^2
Area per lipid, lower leaflet : 0.583197761890625 nm^2

Writing Area per lipid...
Done!

To me, it looks like it is not looking at the 126 lipids that I updated in the 
topology file. H


OK, I seem to remember 124 being what my system produced, but that's irrelevant. 
 Check out the lines above.



Erica


From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998244...@n6.nabble.com]
Sent: Friday, June 08, 2012 5:21 PM
To: Hicks, Erica
Subject: RE: Energy Minimization - not getting correct lipid area



On 6/8/12 6:18 PM, Erica Hicks wrote:

Hi,

Everything should be updated correctly. I added in the DPPC 128 underneath
the protein in [molecules] but I still get the same results. What do you mean
by  Further manual modifications are necessary based on how many lipids
InflateGRO removes? After I generated the new position restrain file, I
updated the minim.mdp withe the correct info. I then scaled by a factor of 4,
updated [molecules], ran energy minimization (mdrun -v -deffnm em), and


This is all my comment meant.  If InflateGRO removes 4 lipids, then you have 124
left, which it sounds like you have accounted for.


scaled by a factor 0.95. I have no idea what could possibly going wrong.
Maybe something with the 

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

[Justin A. Lemkul]

On 6/8/12 6:54 PM, Erica Hicks wrote:

How would I know what coordinate file to use? I have been following the
tutorial word for word. However, I did not get the confout.gro file that I
should have gotten after the minimization (mdrun -v -deffnm em) so I have
been using em.gro. Would this be a problem?


No, confout.gro assumes you're using default names.  The em.gro file you 
obtained is correct.  I have no idea how it's got 128 lipids in it though. 
Check its contents.  If it has 128 lipids, you used an incorrect coordinate file 
for grompp to prepare em.tpr.  That's about the only thing I can think that has 
gone wrong.


-Justin



From: Justin A. Lemkul [via GROMACS]
[ml-node+s5086n4998247...@n6.nabble.com] Sent: Friday, June 08, 2012 5:42 PM
To: Hicks, Erica Subject: RE: Energy Minimization - not getting correct lipid
area



On 6/8/12 6:33 PM, Erica Hicks wrote:


Hi,

bash-3.2$ perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5
area.dat Reading. Scaling lipids There are 128 lipids... with 50
atoms per lipid..

Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids
in the lower leaflet

Centering protein Checking for overlap ...this might actually take
a while 100 % done... There are 2 lipids within cut-off range... 1 will
be removed from the upper leaflet... 1 will be removed from the lower
leaflet...

Writing scaled bilayer   centered protein...


Calculating Area per lipid... Protein X-min/max: 2640 Protein
Y-min/max: 2539 X-range: 14 AY-range: 14 A Building 14 X 14 2D grid
on protein coordinates... Calculating area occupied by protein.. full
TMD.. upper TMD lower TMD Area per protein: 2 nm^2 Area per lipid:
10.4716089904762 nm^2

Area per protein, upper half: 1.75 nm^2 Area per lipid, upper leaflet :
10.475577244 nm^2

Area per protein, lower half: 2 nm^2 Area per lipid, lower leaflet :
10.4716089904762 nm^2

Writing Area per lipid... Done!

bash-3.2$ mdrun -v -deffnm em Back Off! I just backed up em.log to
./#em.log.6# Getting Loaded... Reading file em.tpr, VERSION 4.5.4 (single
precision) Starting 4 threads Loaded with Money

Making 1D domain decomposition 4 x 1 x 1

Back Off! I just backed up em.trr to ./#em.trr.6#

Back Off! I just backed up em.edr to ./#em.edr.6#

Steepest Descents: Tolerance (Fmax)   =  1.0e+03 Number of steps=
5 Step=0, Dmax= 1.0e-02 nm, Epot= -3.06212e+05 Fmax= 5.37269e+03,
atom= 3275 Step=1, Dmax= 1.0e-02 nm, Epot= -3.10498e+05 Fmax=
2.40668e+03, atom= 3024 Step=3, Dmax= 6.0e-03 nm, Epot= -3.10958e+05
Fmax= 2.89119e+03, atom= 4225 Step=5, Dmax= 3.6e-03 nm, Epot=
-3.12589e+05 Fmax= 1.46767e+03, atom= 1365 Step=6, Dmax= 4.3e-03 nm,
Epot= -3.13033e+05 Fmax= 3.83969e+03, atom= 1365 Step=7, Dmax= 5.2e-03
nm, Epot= -3.13599e+05 Fmax= 2.88720e+03, atom= 1365 Step=8, Dmax=
6.2e-03 nm, Epot= -3.13688e+05 Fmax= 4.93154e+03, atom= 1365 Step=9,
Dmax= 7.5e-03 nm, Epot= -3.14101e+05 Fmax= 4.72541e+03, atom= 1365 Step=
11, Dmax= 4.5e-03 nm, Epot= -3.14800e+05 Fmax= 9.90227e+02, atom= 1365

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.6#

Steepest Descents converged to Fmax   1000 in 12 steps Potential Energy  =
-3.1480012e+05 Maximum force =  9.9022711e+02 on atom 1365 Norm of
force =  1.2180042e+02


bash-3.2$ perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat Reading. Scaling lipids There are 128 lipids...


Something is wrong here.  You should only have 126 lipids since 2 were
removed before.  Did you minimize the correct coordinate file?


with 50 atoms per lipid..

Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids
in the lower leaflet

No protein coordinates found...


This is also strange.  This, coupled with the lines above regarding the
number of lipids, suggest you're using the wrong coordinate file.


Writing scaled bilayer   centered protein...


Calculating Area per lipid... Protein X-min/max: 1- Protein
Y-min/max: 1- X-range: -1 AY-range: -1 A Building
-1 X -1 2D grid on protein coordinates... Calculating area occupied
by protein.. full TMD.. upper TMD.. lower TMD..


The following areas are meaningless, for reasons associated with incorrect
content or processing thereof.


Area per protein: 0 nm^2 Area per lipid: 0.583197761890625 nm^2

Area per protein, upper half: 0 nm^2 Area per lipid, upper leaflet :
0.583197761890625 nm^2

Area per protein, lower half: 0 nm^2 Area per lipid, lower leaflet :
0.583197761890625 nm^2

Writing Area per lipid... Done!

To me, it looks like it is not looking at the 126 lipids that I updated in
the topology file. H


OK, I seem to remember 124 being what my system produced, but that's
irrelevant. Check out the lines above.


Erica

 From: Justin A. Lemkul [via GROMACS]
[[hidden 

Re: [gmx-users] First Energy Minimization in a MD

[Justin A. Lemkul]

On 5/12/12 4:25 PM, Lara Bunte wrote:

Hello

I read the mdp options more than once but I don't understand how to make a good 
em.mdp file for the first energy minimization, if you plug your molecule in a 
water box. In my tutorial is this example given.

integrator = steep
nsteps = 200


This is a relatively small number of steps.  Even fairly standard proteins in 
water often require more iterations in EM.



nstlist = 10


You should always set nstlist to 1 for EM.


rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
nstenergy = 10




You do not set any values for emstep or emtol, so you're trusting that the 
defaults are desirable.  The default value for emtol is 10 kJ mol^-1 nm^-1, 
which is often very difficult (if not impossible) to achieve with the steepest 
descents algorithm in single precision.  It is also often unnecessary.


The result of specifying a very low emtol and relatively few steps is that your 
EM is likely to end prematurely, before actually converging.



1.) Is it possible to use this as a standard for all first energy minimization.



No, for the reasons listed above.  In addition, your settings regarding cutoffs, 
electrostatics methods, etc should be based on what your force field requires. 
Thus, there is no universal .mdp file for any simulation process.  In reality, 
during EM the differences will likely be small.  The goal of EM is to produce a 
reasonable starting configuration that can be subsequently equilibrated. 
However, if your .mdp files are wildly different between these two processes, 
you may get unexpected results due to differences in the way the potential (and 
as a result, the forces) is evaluated.



2.) Is the choose of parameters here dependent on the force field? I use a 
CHARMM27, do you think I should change something?



Perhaps.  What does your literature reading regarding CHARMM27 tell you are 
appropriate settings?  Particularly important are the cutoffs and vdW method. 
Typically a plain cutoff is not used with CHARMM force fields; a shift function 
is recommended.



3.) What are the criteria to choose these parameters? As I said I read the mdp 
options, so I know what this Option above mean, but I don't know how to know 
that this are the right parameters?

To say my question in other words: How do I know how the em.mdp file has to 
look like?



The biggest factor is the force field itself and what it requires, as is true 
for all simulation process, EM or otherwise.


-Justin

--


Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] running energy minimization error

[Justin A. Lemkul]

xiaojiong wrote:

Dear,
I have finished the command 
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat,the 
I want to run energy minimization.I submit the command grompp -f 
minim.mdp -c system_inflated.gro -p topol.top -o em.tpr.The error like this

 Back Off!Ijust backed up mdout.mdp to ./#mdout.mdp.4#
Generated 813 of the 2346 non-bonded parameter combinations
WARING 1 [file drg.itp,line1]:
Too few parameters on line (source file toppush.c, line 1501)

WARING 2 [file drg.itp,line2]:
Too few parameters on line (source file toppush.c, line 1501)

WARING 3 [file drg.itp,line17]:
Too few parameters on line (source file toppush.c, line 1501)

ERROR 1 [file drg.itp,line 21]:
Expected a molecule type name and nrexcl

Program grompp, VERSION 4.5.3
Source code file:toppush.c, line:1187

Fatal error:
Atomtype \par not found



Your .itp file does not conform to the required format.  See Chapter 5 of the 
manual.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error energy minimization on protein with implicit water

[lina]

On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote:

 Dear Gromacs users,

 I have a MD simulated protein and i take frame from this and remove water
 and add water implicit in the interface and want to do energy minimization
 but while doing the minimization i get errors. The steps followed are-

 pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
 grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr

 The minim.mdp file =

 ; Lines starting with ';' ARE COMMENTS
 ; Everything following ';' is also comment

 title        = Energy Minimization    ; Title of run

 ; The following line tell the program the standard locations where to find
 certain files
 cpp        = /lib/cpp    ; Preprocessor

 ; Define can be used to control processes
 define  = -DFLEXIBLE

 ; Parameters describing what to do, when to stop and what to save
 integrator    = steep        ; Algorithm (steep = steepest descent
 minimization)
 emtol        = 1000.0    ; Stop minimization when the maximum force  1.0
emtol = 1.0
 kJ/mol
 nsteps        = 5000        ; Maximum number of (minimization) steps to
 perform
 nstenergy    = 1        ; Write energies to disk every nstenergy steps
 energygrps    = System    ; Which energy group(s) to write to disk

 ; Parameters describing how to find the neighbors of each atom and how to
 calculate the interactions
 ns_type        = simple      ; Method to determine neighbor list (simple,
 grid)
 coulombtype    = cut-off      ; Treatment of long range electrostatic
 interactions
 rcoulomb    = 1.0        ; long range electrostatic cut-off
 rvdw        = 1.0        ; long range Van der Waals cut-off
 constraints    = none        ; Bond types to replace by constraints
 pbc        = no        ; Periodic Boundary Conditions (yes/no)

 I get a note as =
 System has non-zero total charge: -4.96e+00

 then i tried using genion step as=

 genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log

 then again the grompp step and mdrun .
 but while doing mdrun i get an error as=

 Stepsize too small, or no change in energy.
 Converged to machine precision,
 but not to the requested precision Fmax  1000


 but here i have given nsteps as 5000 so why does it stop.
 --
 Aiswarya  B Pawar

 Project Assistant,
 Bioinformatics Dept,
 Indian Institute of Science
 Bangalore



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Re: [gmx-users] Error energy minimization on protein with implicit water

[Justin A. Lemkul]

lina wrote:

On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote:

Dear Gromacs users,

I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-

pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr

The minim.mdp file =

; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title= Energy Minimization; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp= /lib/cpp; Preprocessor

; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0; Stop minimization when the maximum force  1.0

emtol = 1.0


If mdrun could not converge to 1000, setting a target of 1 will not solve 
anything.  The OP should refer to:


http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error energy minimization on protein with implicit water

[aiswarya pawar]

By setting the emtol to 1.0, didnt work. Anyother way i could figure out.

On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 lina wrote:

 On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com
 wrote:

 Dear Gromacs users,

 I have a MD simulated protein and i take frame from this and remove water
 and add water implicit in the interface and want to do energy
 minimization
 but while doing the minimization i get errors. The steps followed are-

 pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
 grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr

 The minim.mdp file =

 ; Lines starting with ';' ARE COMMENTS
 ; Everything following ';' is also comment

 title= Energy Minimization; Title of run

 ; The following line tell the program the standard locations where to
 find
 certain files
 cpp= /lib/cpp; Preprocessor

 ; Define can be used to control processes
 define  = -DFLEXIBLE

 ; Parameters describing what to do, when to stop and what to save
 integrator= steep; Algorithm (steep = steepest descent
 minimization)
 emtol= 1000.0; Stop minimization when the maximum force  1.0

 emtol = 1.0


 If mdrun could not converge to 1000, setting a target of 1 will not solve
 anything.  The OP should refer to:

 http://www.gromacs.org/**Documentation/Errors#Stepsize_**
 too_small.2c_or_no_change_in_**energy._Converged_to_machine_**
 precision.2c_but_not_to_the_**requested_precisionhttp://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

 -Justin

 --
 ==**==

 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==

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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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Re: [gmx-users] divergent energy minimization results from identical starting system

[Roland Schulz]

Hi,

are you running in parallel (either MPI or threads)? Load-balancing is one
reason for different rounding errors.
You can run with mdrun -reprod to avoid any different rounding between
runs and should in general get the same then.

Roland

On Fri, Jan 28, 2011 at 6:17 PM, Matthew Chan mch...@connect.carleton.cawrote:

 Hi,

 My second question is about the divergent energy minimization results which
 I have been receiving.

 I've taken the 1AKI lysozyme and prepared a single em.tpr file (1AKI is in
 vacuum). Afterwards I make 10 copies of the em.tpr file and use mdrun on
 each one. If I set the stopping condition to less than 1000kJ/mol nm, my
 potential energies and final structures from each run are not identical.

 I've tried both steepest descent and cg methods for minimization. I've also
 checked that the Fmax is indeed less than my stopping condition, and the
 potential energy is negative. Is this problem well documented or is there
 something wrong with my system? There seem to be a few parts of the manual
 that allude to the possibility of variance between subsequent runs of EM.

 If this is a well documented problem, can someone try explaining the cause
 to me please? I would like to learn more about this topic.

 Also, the potential energy value reported seems to be several orders of
 magnitude different from what other programs are reporting (24 000 vs 500).
 What units are it expressed in?

 Thanks in advance for your replies,

 --
 

 Matthew Chan


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Re: [gmx-users] divergent energy minimization results from identical starting system

[Matt Chan]

Hi Roland,

Ah, the -reprod option makes everything consistent between runs now. The 
term 'binary reproducibility' in the help message was a bit confusing at 
first, but I found the wiki page on reproducibility.


Thanks for your help,
Matt

On 01/28/2011 06:29 PM, Roland Schulz wrote:

Hi,

are you running in parallel (either MPI or threads)? Load-balancing is 
one reason for different rounding errors.
You can run with mdrun -reprod to avoid any different rounding 
between runs and should in general get the same then.


Roland

On Fri, Jan 28, 2011 at 6:17 PM, Matthew Chan 
mch...@connect.carleton.ca mailto:mch...@connect.carleton.ca wrote:


Hi,

My second question is about the divergent energy minimization
results which I have been receiving.

I've taken the 1AKI lysozyme and prepared a single em.tpr file
(1AKI is in vacuum). Afterwards I make 10 copies of the em.tpr
file and use mdrun on each one. If I set the stopping condition to
less than 1000kJ/mol nm, my potential energies and final
structures from each run are not identical.

I've tried both steepest descent and cg methods for minimization.
I've also checked that the Fmax is indeed less than my stopping
condition, and the potential energy is negative. Is this problem
well documented or is there something wrong with my system? There
seem to be a few parts of the manual that allude to the
possibility of variance between subsequent runs of EM.

If this is a well documented problem, can someone try explaining
the cause to me please? I would like to learn more about this topic.

Also, the potential energy value reported seems to be several
orders of magnitude different from what other programs are
reporting (24 000 vs 500). What units are it expressed in?

Thanks in advance for your replies,

-- 



Matthew Chan


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Re: [gmx-users] Targeted Energy Minimization

[Mark Abraham]

On 5/11/2010 4:53 PM, Yao Yao wrote:

Hi Gmxers,

Is that possible that in mdp file, only a specifically-targeted part 
inside/of the protein is energy minimized (EM)? Like, just wanna EM 
the ligand or one out of the two proteins in protein-docking.




I'm not sure, but freeze groups + EM might do this. See manual.

Mark


Thanks in advance,

Yao




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Re: [gmx-users] grompp, energy minimization,, output file error

[Mark Abraham]

On 23/04/2010 8:52 AM, Moeed wrote:

Dear gmx users,

I am trying to run grompp program to preprocess the input files. input
gro file contains coordinates of a stack of hexane molecules (256
molecules).

grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em
-maxwarn 30  output.grompp_em


Don't use -maxwarn unless you know why the warnings may be ignored.


my problem is that output: Hexane_em.tpr contains strange notations:

é...@!`a‰7kÇ?ýÐå`a...@!(r° Äœ@(LÍ?û i�...@!o\(õ @(LÍ?ù n— o...@!
¾vÈ´9@(lÍ?öí‘hr...@!f§ï ²-@(lÍ?ôýó¶e�...@!


It's a binary file. Don't try to read it with a text reader. GROMACS 
provides the gmxdump utility to get at the information, but that won't 
help you here.



output.grompp_em:


   GNU nano 2.0.9File: output.grompp_em


Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'HEX'

NOTE 1 [file HexaneModified.top, line 163]:
   System has non-zero total charge: 2.206157e+04


Your system has a charge of 22061.57. This is because you've broken your 
[atoms] section. See below.



processing coordinates...

Warning: atom name 1 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C1)


Another symptom of the above.


Warning: atom name 2 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C2)
Warning: atom name 3 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C3)
Warning: atom name 4 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C4)
Warning: atom name 5 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C5)
Warning: atom name 6 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C6)
Warning: atom name 7 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H1)
Warning: atom name 8 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H2)
Warning: atom name 9 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H3)
Warning: atom name 10 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H4)
Warning: atom name 11 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H5)
Warning: atom name 12 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H6)
Warning: atom name 13 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H7)
Warning: atom name 14 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H8)
Warning: atom name 15 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H9)
Warning: atom name 16 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H10)
Warning: atom name 17 in HexaneModified.top and Hexane-stack.gro does
not match (1 - H11)

WARNING 1 [file HexaneModified.top, line 163]:
   5120 non-matching atom names
   atom names from HexaneModified.top will be used
   atom names from Hexane-stack.gro will be ignored


double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

NOTE 2 [file HexaneModified.top, line unknown]:
   The largest charge group contains 20 atoms.
   Since atoms only see each other when the centers of geometry of the
charge
   groups they belong to are within the cut-off distance, too large charge
   groups can lead to serious cut-off artifacts.
   For efficiency and accuracy, charge group should consist of a few atoms.
   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


Another symptom.


initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat

Making dummy/rest group for T-Coupling containing 5120 elements
Making dummy/rest group for Acceleration containing 5120 elements
Making dummy/rest group for Freeze containing 5120 elements
Making dummy/rest group for Energy Mon. containing 5120 elements
Making dummy/rest group for VCM containing 5120 elements
Number of degrees of freedom in T-Coupling group rest is 15357.00
Making dummy/rest group for User1 containing 5120 elements
Making dummy/rest group for User2 containing 5120 elements
Making dummy/rest group for XTC containing 5120 elements
Making dummy/rest group for Or. Res. Fit containing 5120 elements
Making dummy/rest group for QMMM containing 5120 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest

Checking consistency between energy and charge groups...

NOTE 3 [file em.mdp, line unknown]:
   You are using a plain Coulomb cut-off, which might produce artifacts.
   You might want to consider 

Re: [gmx-users] grompp, energy minimization,, output file error

[Justin A. Lemkul]

Moeed wrote:

Dear gmx users,

I am trying to run grompp program to preprocess the input files. input 
gro file contains coordinates of a stack of hexane molecules (256 
molecules).


grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em 
-maxwarn 30  output.grompp_em



my problem is that output: Hexane_em.tpr contains strange notations:

é...@!`a‰7kÇ?ýÐå`a...@!(r° Äœ@(LÌÌÌÌÍ?û iÂ...@!o\(õ @(LÌÌÌÌÍ?ù n— o...@! 
¾vÈ´9@(lÌÌÌÌÍ?öí‘hr...@!f§ï ²-@(lÌÌÌÌÍ?ôýó¶eÂ...@!





A .tpr file is binary.  You won't be able to read it.


output.grompp_em:


  GNU nano 2.0.9File: 
output.grompp_em   



Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'HEX'

NOTE 1 [file HexaneModified.top, line 163]:
  System has non-zero total charge: 2.206157e+04



This line is very concerning.  You have a net charge in excess of +22000! 
Something is badly broken in your topology.





processing coordinates...

Warning: atom name 1 in HexaneModified.top and Hexane-stack.gro does not 
match (1 - C1)


These errors all indicate that you either have something out of order in your 
[molecules] directive (it has to match the order of the molecules in the 
coordinate file) or you have an improperly-formatted coordinate file.


snip



NOTE 2 [file HexaneModified.top, line unknown]:
  The largest charge group contains 20 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.



See the manual for the group concept.  Large charge groups can cause bad 
electrostatics artifacts.



initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat

Making dummy/rest group for T-Coupling containing 5120 elements
Making dummy/rest group for Acceleration containing 5120 elements
Making dummy/rest group for Freeze containing 5120 elements
Making dummy/rest group for Energy Mon. containing 5120 elements
Making dummy/rest group for VCM containing 5120 elements
Number of degrees of freedom in T-Coupling group rest is 15357.00
Making dummy/rest group for User1 containing 5120 elements
Making dummy/rest group for User2 containing 5120 elements
Making dummy/rest group for XTC containing 5120 elements
Making dummy/rest group for Or. Res. Fit containing 5120 elements
Making dummy/rest group for QMMM containing 5120 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest

Checking consistency between energy and charge groups...

NOTE 3 [file em.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.



There is also very little justification for using plain cutoffs.  Heed the 
warning and use a more reasonable (and modern) setting.


snip


[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
typeBchargeB  massB
 1   opls_157  1C1  1  -0.18 12.011   ; 
qtot -0.18
 2   opls_158  1C2  1  -0.12 12.011   ; 
qtot -0.3
 3   opls_158  1C3  1  -0.12 12.011   ; 
qtot -0.42
 4   opls_158  1C4  1  -0.12 12.011   ; 
qtot -0.54
 5   opls_158  1C5  1  -0.12 12.011   ; 
qtot -0.66
 6   opls_157  1C6  1  -0.18 12.011   ; 
qtot -0.84
 7   opls_140  1H1  1   0.06  1.008   ; 
qtot -0.78
 8   opls_140  1H2  1   0.06  1.008   ; 
qtot -0.72
 9   opls_140  1H3  1   0.06  1.008   ; 
qtot -0.66
10   opls_140  1H4  1   0.06  1.008   ; 
qtot -0.6
11   opls_140  1H5  1   0.06  1.008   ; 
qtot -0.54
12   opls_140  1H6  1   0.06  1.008   ; 
qtot -0.48
13   opls_140  1H7  1   0.06  1.008   ; 
qtot -0.42
14   opls_140  1H8  1   0.06  1.008   ; 
qtot -0.36
15   opls_140  1H9  1   

RE: [gmx-users] grompp, energy minimization,, output file error

[Dallas B. Warren]

For starters there is no residue name in your .gro file, you simply have a 
number.  First column should be …

1HEX  C1
1HEX C2
.
.
.
1HEX H14
2HEX C1

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
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Re: [gmx-users] an energy minimization question, working with H-BONDS

[Justin A. Lemkul]

Miguel Quiliano Meza wrote:

Dear Users.
 
I am a relative new user of GROMACS and I have some doubts:
 
I would like to perform a energy minimization (with water and iones) of 
a crystal in orden to re-build the H-bonds responsible of the secundary 
structure, to achieve this goal I want to restraint the movement of the 
protein (aminoacids) and permit the movement of the H-bonds as a 
product of add Hydrogens with pdb2gmx.
 
I think that this task could be define/establish in CONSTRAINS in 
the .mdp file, I searched in the web and only find this:
 


First, understand that a constraint and a restraint are very different 
concepts in Gromacs:


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

Thus, the constraints keyword is unrelated to what you're looking to do.

Simple energy minimization will seek to relax the structure, forming favorable 
contacts and resolving large forces.  Whether or not this bears any useful 
information about the stability of secondary structure is debatable.  Running 
true MD is a better tool for that purpose, but EM should suffice to form any 
hydrogen bonds that are reasonably close in space.


I don't think it will be meaningful at all to restrain part of the protein and 
hope that hydrogen bonds in the backbone re-orient.  You'd essentially be fixing 
the side chain positions, which will not allow for much re-organization, not 
that I'd expect to see major changes during EM, anyway.


-Justin




  Bonds


constraints:

*none*
No constraints except for those defined explicitly in the
topology, i.e. bonds are represented by a harmonic (or other)
potential or a Morse potential (depending on the setting of
*morse*) and angles by a harmonic (or other) potential. 
*hbonds*
Convert the bonds with H-atoms to constraints. 
*all-bonds*
Convert all bonds to constraints. 
*h-angles*

Convert all bonds and additionally the angles that involve
H-atoms to bond-constraints. 
*all-angles*
Convert all bonds and angles to bond-constraints. 

What option shoud I use for my objective? My objetive, is it possible to 
do? I would be very grateful if someone can help me with some ideas or 
advices.


thanks in advance

Miguel



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: Energy minimization output

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:


This is upto 40 ns after that i am not getting anything like that. I don't
know exactly what it mean and how could i get rid of such messages.I don't
know how to deal with it.


What it means is that you had some nasty contacts between some elements of your 
system and the surrounding water.  If the messages do indeed go away during EM, 
and the potential energy levels off to a reasonable, negative value, then things 
should be fine to proceed.


-Justin



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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] Re: Energy minimization output

[Kukol, Andreas]

Your output looks like, that you are doing MD simulations, because a time in ps 
is reported. You should do energy minimisation first, use 'integrator = steep' 
in your .mdp file

Andreas

 -Original Message-
 From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
 On Behalf Of [EMAIL PROTECTED]
 Sent: 13 August 2008 10:26
 To: gmx-users@gromacs.org
 Subject: [gmx-users] Re: Energy minimization output

 Hi

 I am doing a 5 peptide simulation.

 I have done energy minimization using this command


 1.grompp -v -f em.mdp -c b4em_sol_mov1.gro -p gnnqqny.top -o em.tpr -nice 19

 2.mdrun -v -s em.tpr -e em.edr -c after_em.gro -o em.trr -g em.log -nice 19


 After energy minimization (steep, 5000 steps, emtol 100) i am getting some
 pdb files referring to different steps of energy minimization as
 outputalong with other standard output. when i checked the em.log file i
 am getting




Step   Time Lambda
  15   15.00.0


 t = 0.015 ps: Water molecule starting at atom 8264 can not be settled.
 Check for bad contacts and/or reduce the timestep.Wrote pdb files with
 previous and current coordinates
Step   Time Lambda
  16   16.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 9.98333e+041.36695e+041.52668e+031.78607e+034.70247e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.55150e+033.77075e+05   -3.15610e+05   -2.36704e+041.61864e+05
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00


 t = 0.017 ps: Water molecule starting at atom 15071 can not be settled.
 Check for bad contacts and/or reduce the timestep.Wrote pdb files with
 previous and current coordinates
Step   Time Lambda
  17   17.00.0

Step   Time Lambda
  18   18.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 9.45661e+041.37081e+041.40906e+031.82338e+033.67231e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.53132e+033.24723e+05   -3.17639e+05   -2.36512e+041.01143e+05
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00

Step   Time Lambda
  19   19.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 8.03329e+041.30736e+041.41046e+031.92183e+033.32668e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.50827e+032.64074e+05   -3.15758e+05   -2.36011e+042.72885e+04
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00

Step   Time Lambda
  20   20.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 6.75745e+041.25722e+041.34546e+031.92589e+033.23734e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.47910e+032.34231e+05   -3.18011e+05   -2.35785e+04   -1.82240e+04
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00


 t = 0.021 ps: Water molecule starting at atom 15071 can not be settled.
 Check for bad contacts and/or reduce the timestep.Wrote pdb files with
 previous and current coordinates
Step   Time Lambda
  21   21.00.0

Step   Time Lambda
  22   22.00.0

Energies (kJ/mol)
Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
 5.69021e+041.19959e+041.30660e+031.92492e+033.11441e+03
  Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
 2.47034e+032.13147e+05   -3.18361e+05   -2.35596e+04   -5.10587e+04
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 0.0e+000.0e+000.0e+000.0e+00


 This is upto 40 ns after that i am not getting anything like that. I don't
 know exactly what it mean and how could i get rid of such messages.I don't
 know how to deal with it.

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Re: [gmx-users] complete energy minimization

[Mark Abraham]

Justin A. Lemkul wrote:

Quoting s lal badshah [EMAIL PROTECTED]:


Dear experts,
Hi! I minimized the system and gies 10,000 nsteps, but the output is:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  1000.
Potential Energy  = -1.9742134e+21
Maximum force =  4.1648520e+06 on atom 1934
Norm of force =  5.6557945e+06

What other method I should adopt? or what type of correction I should do ? so
that minimization is complete. As  before I also did this minimization and
then in equilibration it gives faults to me. I read the errors gromacs pages
from net but didn't reached to any conclusion. What are the other methods of
minimization? Is it creat any problem for me in equilibration?
Your guidance will be highly appreciated.


There is nothing wrong with this minimization output.  The process completed and
left you with a negative potential energy, which is what you're after.  What
might be more useful is a better description of what you are doing and the
faults that you are getting during equilibration.

What is in your system?  What force field are you using?  What is in your .mdp
file?  Providing this type of information will help us to help you.


I agree with Justin, except that the magnitude of the PE and forces are 
far larger than one would normally see for a few thousand atoms in a 
condensed-phase system. This suggests some gross problem. However since 
we don't know what the system is, our hands are a bit tied when diagnosing.


Mark
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Re: [gmx-users] CG energy minimization

[Mark Abraham]

Myunggi Yi wrote:

Dear users,

I'd like to restraint the protein during the minimization.
I've got the following message.


In GROMACS, restraints are different from constraints. Check out the 
manual for details.



ERROR: can not do Conjugate Gradients with constraints


Your .top is defining some constraints, and if you'd checked out the 
manual, you'd have confirmed that GROMACS can't handle constraints with 
the CG algorithm.



em.mdp file
+
cpp  = cpp
include  =
define   = -DPOSRES
define   = -DFLEXIBLE

; RUN CONTROL PARAMETERS
integrator   = cg
; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 250
+

How can I do this?


Either don't use constraints or don't use CG.

Mark
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Re: [gmx-users] CG energy minimization

[Myunggi Yi]

Thnak you.

I don't use any constrant like lincs or shake.
Why do I get the error message.


On Jan 14, 2008 4:11 PM, Mark Abraham [EMAIL PROTECTED] wrote:

 Myunggi Yi wrote:
  Dear users,
 
  I'd like to restraint the protein during the minimization.
  I've got the following message.

 In GROMACS, restraints are different from constraints. Check out the
 manual for details.

  ERROR: can not do Conjugate Gradients with constraints

 Your .top is defining some constraints, and if you'd checked out the
 manual, you'd have confirmed that GROMACS can't handle constraints with
 the CG algorithm.

  em.mdp file
  +
  cpp  = cpp
  include  =
  define   = -DPOSRES
  define   = -DFLEXIBLE
 
  ; RUN CONTROL PARAMETERS
  integrator   = cg
  ; Start time and timestep in ps
  tinit= 0
  dt   = 0.001
  nsteps   = 250
  +
 
  How can I do this?

 Either don't use constraints or don't use CG.

 Mark
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-- 
Best wishes,

MYUNGGI YI
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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Re: [gmx-users] CG energy minimization

[Myunggi Yi]

Sorry this is my top file.

#include ffgmx.itp
#include ../lipid.popc.itp
#include popc.itp
#include pro.itp
#include ions.itp
#include spc.itp

Which one defines constraints?


On Jan 14, 2008 4:35 PM, Myunggi Yi [EMAIL PROTECTED] wrote:

 Thnak you.

 I don't use any constrant like lincs or shake.
 Why do I get the error message.



 On Jan 14, 2008 4:11 PM, Mark Abraham  [EMAIL PROTECTED] wrote:

  Myunggi Yi wrote:
   Dear users,
  
   I'd like to restraint the protein during the minimization.
   I've got the following message.
 
  In GROMACS, restraints are different from constraints. Check out the
  manual for details.
 
   ERROR: can not do Conjugate Gradients with constraints
 
  Your .top is defining some constraints, and if you'd checked out the
  manual, you'd have confirmed that GROMACS can't handle constraints with
  the CG algorithm.
 
   em.mdp file
   +
   cpp  = cpp
   include  =
   define   = -DPOSRES
   define   = -DFLEXIBLE
  
   ; RUN CONTROL PARAMETERS
   integrator   = cg
   ; Start time and timestep in ps
   tinit= 0
   dt   = 0.001
   nsteps   = 250
   +
  
   How can I do this?
 
  Either don't use constraints or don't use CG.
 
  Mark
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 --
 Best wishes,

 MYUNGGI YI
 ==
 KLB 419
 Institute of Molecular Biophysics
 Florida State University
 Tallahassee, FL 32306

 Office: (850) 645-1334
 http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi




-- 
Best wishes,

MYUNGGI YI
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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Re: [gmx-users] CG energy minimization

[Justin A. Lemkul]

Perhaps this is too obvious to be the solution, but have you considered setting
'constraints = none' in your em.mdp file?  After all, as Mark originally
pointed out, the documentation will tell you that constraints and CG don't mix.

-Justin

Quoting Myunggi Yi [EMAIL PROTECTED]:

 Sorry this is my top file.

 #include ffgmx.itp
 #include ../lipid.popc.itp
 #include popc.itp
 #include pro.itp
 #include ions.itp
 #include spc.itp

 Which one defines constraints?


 On Jan 14, 2008 4:35 PM, Myunggi Yi [EMAIL PROTECTED] wrote:

  Thnak you.
 
  I don't use any constrant like lincs or shake.
  Why do I get the error message.
 
 
 
  On Jan 14, 2008 4:11 PM, Mark Abraham  [EMAIL PROTECTED] wrote:
 
   Myunggi Yi wrote:
Dear users,
   
I'd like to restraint the protein during the minimization.
I've got the following message.
  
   In GROMACS, restraints are different from constraints. Check out the
   manual for details.
  
ERROR: can not do Conjugate Gradients with constraints
  
   Your .top is defining some constraints, and if you'd checked out the
   manual, you'd have confirmed that GROMACS can't handle constraints with
   the CG algorithm.
  
em.mdp file
+
cpp  = cpp
include  =
define   = -DPOSRES
define   = -DFLEXIBLE
   
; RUN CONTROL PARAMETERS
integrator   = cg
; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 250
+
   
How can I do this?
  
   Either don't use constraints or don't use CG.
  
   Mark
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  --
  Best wishes,
 
  MYUNGGI YI
  ==
  KLB 419
  Institute of Molecular Biophysics
  Florida State University
  Tallahassee, FL 32306
 
  Office: (850) 645-1334
  http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi
 



 --
 Best wishes,

 MYUNGGI YI
 ==
 KLB 419
 Institute of Molecular Biophysics
 Florida State University
 Tallahassee, FL 32306

 Office: (850) 645-1334
 http://www.scs.fsu.edu/~myunggi






Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] CG energy minimization

[Myunggi Yi]

Yes, I did (constraints=none).

These are my conclusions.

Since I could do CG without my position restraint,
My .top doesn't include any constraint. (if my posre.itp is not constraint).
The manual says SD is enough for general purpose.
If one wants to do energy minimization with position restraint, then do SD
only.

Thank you anyway.


On Jan 14, 2008 5:21 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote:


 Perhaps this is too obvious to be the solution, but have you considered
 setting
 'constraints = none' in your em.mdp file?  After all, as Mark originally
 pointed out, the documentation will tell you that constraints and CG don't
 mix.

 -Justin

 Quoting Myunggi Yi [EMAIL PROTECTED]:

  Sorry this is my top file.
 
  #include ffgmx.itp
  #include ../lipid.popc.itp
  #include popc.itp
  #include pro.itp
  #include ions.itp
  #include spc.itp
 
  Which one defines constraints?
 
 
  On Jan 14, 2008 4:35 PM, Myunggi Yi [EMAIL PROTECTED] wrote:
 
   Thnak you.
  
   I don't use any constrant like lincs or shake.
   Why do I get the error message.
  
  
  
   On Jan 14, 2008 4:11 PM, Mark Abraham  [EMAIL PROTECTED]
 wrote:
  
Myunggi Yi wrote:
 Dear users,

 I'd like to restraint the protein during the minimization.
 I've got the following message.
   
In GROMACS, restraints are different from constraints. Check out the
manual for details.
   
 ERROR: can not do Conjugate Gradients with constraints
   
Your .top is defining some constraints, and if you'd checked out the
manual, you'd have confirmed that GROMACS can't handle constraints
 with
the CG algorithm.
   
 em.mdp file
 +
 cpp  = cpp
 include  =
 define   = -DPOSRES
 define   = -DFLEXIBLE

 ; RUN CONTROL PARAMETERS
 integrator   = cg
 ; Start time and timestep in ps
 tinit= 0
 dt   = 0.001
 nsteps   = 250
 +

 How can I do this?
   
Either don't use constraints or don't use CG.
   
Mark
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   --
   Best wishes,
  
   MYUNGGI YI
   ==
   KLB 419
   Institute of Molecular Biophysics
   Florida State University
   Tallahassee, FL 32306
  
   Office: (850) 645-1334
   http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi 
 http://www.scs.fsu.edu/%7Emyunggi
  
 
 
 
  --
  Best wishes,
 
  MYUNGGI YI
  ==
  KLB 419
  Institute of Molecular Biophysics
  Florida State University
  Tallahassee, FL 32306
 
  Office: (850) 645-1334
  http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi
 



 

 Justin A. Lemkul
 Graduate Research Assistant
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 [EMAIL PROTECTED] | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

 
 ___
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 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to [EMAIL PROTECTED]
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-- 
Best wishes,

MYUNGGI YI
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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Re: [gmx-users] CG energy minimization

[Mark Abraham]

Justin A. Lemkul wrote:

Perhaps this is too obvious to be the solution, but have you considered setting
'constraints = none' in your em.mdp file?  After all, as Mark originally
pointed out, the documentation will tell you that constraints and CG don't mix.

-Justin


Manual 7.3.17 points out that this usage does not supersede explicit 
constraints.


Mark
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Re: [gmx-users] CG energy minimization

[Mark Abraham]

Myunggi Yi wrote:

Sorry this is my top file.

#include ffgmx.itp
#include ../lipid.popc.itp
#include popc.itp
#include pro.itp
#include ions.itp
#include  spc.itp

Which one defines constraints?


See manual section five for the other ways of defining constraints. 
You'll have to do your own detective work on those files, or the rest of 
 your .top file.


Mark
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Re: [gmx-users] CG energy minimization

[Xavier Periole]

On Mon, 14 Jan 2008 17:41:13 -0500
 Myunggi Yi [EMAIL PROTECTED] wrote:

Yes, I did (constraints=none).

These are my conclusions.

Since I could do CG without my position restraint,


Are you sure you do CG simulations? your includes indicates you don't!


My .top doesn't include any constraint. (if my posre.itp is not constraint).
The manual says SD is enough for general purpose.
If one wants to do energy minimization with position restraint, then do SD
only.


You want to do stochastic dynamics (SD) or energy minimization (steep)?

Your message is confusing ...

XAvier
 


Thank you anyway.


On Jan 14, 2008 5:21 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote:



Perhaps this is too obvious to be the solution, but have you considered
setting
'constraints = none' in your em.mdp file?  After all, as Mark originally
pointed out, the documentation will tell you that constraints and CG don't
mix.

-Justin

Quoting Myunggi Yi [EMAIL PROTECTED]:

 Sorry this is my top file.

 #include ffgmx.itp
 #include ../lipid.popc.itp
 #include popc.itp
 #include pro.itp
 #include ions.itp
 #include spc.itp

 Which one defines constraints?


 On Jan 14, 2008 4:35 PM, Myunggi Yi [EMAIL PROTECTED] wrote:

  Thnak you.
 
  I don't use any constrant like lincs or shake.
  Why do I get the error message.
 
 
 
  On Jan 14, 2008 4:11 PM, Mark Abraham  [EMAIL PROTECTED]
wrote:
 
   Myunggi Yi wrote:
Dear users,
   
I'd like to restraint the protein during the minimization.
I've got the following message.
  
   In GROMACS, restraints are different from constraints. Check out the
   manual for details.
  
ERROR: can not do Conjugate Gradients with constraints
  
   Your .top is defining some constraints, and if you'd checked out the
   manual, you'd have confirmed that GROMACS can't handle constraints
with
   the CG algorithm.
  
em.mdp file
+
cpp  = cpp
include  =
define   = -DPOSRES
define   = -DFLEXIBLE
   
; RUN CONTROL PARAMETERS
integrator   = cg
; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 250
+
   
How can I do this?
  
   Either don't use constraints or don't use CG.
  
   Mark
   ___
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   http://www.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search before
   posting!
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   www interface or send it to [EMAIL PROTECTED]
   Can't post? Read http://www.gromacs.org/mailing_lists/users.php
  
 
 
 
  --
  Best wishes,
 
  MYUNGGI YI
  ==
  KLB 419
  Institute of Molecular Biophysics
  Florida State University
  Tallahassee, FL 32306
 
  Office: (850) 645-1334
  http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi 
http://www.scs.fsu.edu/%7Emyunggi
 



 --
 Best wishes,

 MYUNGGI YI
 ==
 KLB 419
 Institute of Molecular Biophysics
 Florida State University
 Tallahassee, FL 32306

 Office: (850) 645-1334
 http://www.scs.fsu.edu/~myunggi http://www.scs.fsu.edu/%7Emyunggi






Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


___
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--
Best wishes,

MYUNGGI YI
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi


-
XAvier Periole - PhD

NMR  Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-
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[gmx-users] Re: \\[gmx\\-users\\] The energy minimization\\.\\.\\.\\.

[TJ Piggot]

As i say keep things to the list please.

With regards to the files no as you should be able to fix the problem on 
your own as this will help you more in the long run. Try redoing every step 
making sure you do it correctly (especially the editing of the .rtp file)


Tom

--On 18 August 2007 10:58 +0800 MoJie Duan [EMAIL PROTECTED] wrote:


Hi,tom:
Thank you for you help!
Could you provid me the run file about the EM of my ATP molecule? (the
.gro, .top, and .gro.top files after editconf, the .tpr after grompp...
maybe also the ff**.trp and ff*.hdb you used). I will check which
step have problems.

And if i solve this problem, i will introduce my experience of resolving
this problem in gmx-user for the beginner.

Best regards!
Duan


Hi

I just quickly checked and your ATP pdb file works fine for me (it did
have
some weird characters in it that i had to delete, not sure if this was
caused by pasting it into an email). I should point out that this pdb
file
is incomplete as you are missing some hydrogen atoms (pdb2gmx should tell
you this if you modified your .rtp file correctly). See any of the
GROMOS96
.rtp file ATP entries for the hydrogens you have missed that still are
included in a united atom ff.

Also your .mdp parameters work fine with your pdb file so i have no idea
what is going wrong when you try! Check you have modified the .rtp file
correctly and are supplying sensible commands to
pdb2gmx/editconf/grompp/mdrun are the last things i can suggest.

Good luck

Tom

--On 18 August 2007 08:17 +0800 MoJie Duan wrote:


Hi,Tom:
Thank you for your reply!
Before the minimization, I just change the atoms name of ATP, so it can
coordinated to the names in ffG43b1 (the atoms name of ATP in ffG43b1
also changed, each atom have a three-letter name).

My coordinate file (.pdb) was obtained from RCSB PDB, I extracted the xyz
coordinates of ATP molecule from the a .pdb file of a protein, as
following:
___
HETATM 7577 PG ATP 800 -4.997 4.425 -2.604 1.00

 gt; 33.08 P

HETATM 7578 O1G ATP 800 -5.685 5.603 -1.764 1.00
33.76 O
HETATM 7579 O2G ATP 800 -3.427 4.765 -2.665 1.00 32.63
0; O
HETATM 7580 O3G ATP 800 -5.273 3.100 -1.967 1.00
33.16 O
HETATM 7581 PB ATP 800 -5.173 3.787 -5.388 1.00
34.37 P
HETATM 7582 O1B ATP 800 -3.985 4.318 -6.120 1.00
33.33 O
HETATM 7583 O2B ATP 800 -5.232 2.335 -5.045 1.00
33.33 O
HETATM 7584 O3B ATP 800 -5.529 4.675 -4.089 1.00
33.22 O
HETATM 7585 PA ATP 800 -7.773 3.348 -6.436 1.00
35.04 P
HETATM 7586 O1A ATP 800 -8.260 2.720 -5.177 1.00
33.60 O
HETATM 7587 O2A ATP 800 -7.501 2.503 -7.632 1.00
32.64 O
HETATM 7588 O3A ATP 800 -6.483 4.274 -6.168 1.00
34.07 O
HETATM 7589 O5' ATP 800 -8.787 4.518 0; -6.833 1.00
36.40 O
HETATM 7590 C5' ATP 800 -8.403 5.464 -7.846 1.00
39.10 C
HETATM 7591 C4' ATP 800 -9.604 6.315 -8.269 1.00
41.61 C
HETATM 7592 O4' ATP 800 -10.793 5.471 -8.462 1.00
42.22 O
HETATM 7593 C3' ATP 800 -9.937 7.303 -7.152 1.00
41.81 C
HETATM 7594 O3' ATP 800 -10.228 8.5 59 -7.756 1.00
43.61 O
HETATM 7595 C2' ATP 800 -11.191 6.724 -6.514 1.00
42.05 C
HETATM 7596 O2' ATP 800 -12.023 7.764 -6.036 1.00
41.49 O
HETATM 7597 C1' ATP 800 -11.875 6.025 -7.679 1.00
42.90 C
HETATM 7598 N9 ATP 800 -12.608 4.832 -7.218 1.00
43.53 N
HETATM 7599 C8 ATP 800 -12.077 3. 810 -6.547 1.00
43.35 C
HETATM 7600 N7 ATP 800 -13.023 2.904 -6.309 1.00
44.02 N
HETATM 7601 C5 ATP 800 -14.162 3.341 -6.835 1.00
44.22 C
HETATM 7602 C6 ATP 800 -15.461 2.828 -6.899 1.00
44.02 C
HETATM 7603 N6 ATP 800 -15.751 1.647 -6.351 1.00
43.35 N
HETATM 7604 N1 ATP 800 -16.41 4 3.547 -7.525 1.00
43.25 N
HETATM 7605 C2 ATP 800 -16.125 4.717 -8.076 1.00
43.37 C
HETATM 7606 N3 ATP 800 -14.902 5.230 -8.032 1.00
43.76 N
HETATM 7607 C4 ATP 800 -13.901 4.571 -7.417 1.00
44.09 C


and then changed the atoms name:


HETATM 7577 APG ATP 800 -4.997 4.425 -2.604 #160; 1.00
33.08 P
HETATM 7578 OG1 ATP 800 -5.685 5.603 -1.764 1.00
33.76 O
HETATM 7579 OG2 ATP 800 -3.427 4.765 -2.665 1.00
32.63 O
HETATM 7580 OG3 ATP 800 -5.273 3.100 -1.967 1.00
33.16 O
HETATM 7581 APB ATP 800 -5.173 3.787 -5.388 1.00
34.37 P
HETATM 7582 OB1 ATP 800 -3.985 4.3 18 -6.120 1.00
33.33 O
HETATM 7583 OB2 ATP 800 -5.232 2.335 -5.045 1.00
33.33 O
HETATM 7584 OB3 ATP 800 -5.529 4.675 -4.089 1.00
33.22 O
HETATM 7585 APA ATP 800 -7.773 3.348 -6.436 1.00
35.04 P
HETATM 7586 OA1 ATP 800 -8.260 2.720 -5.177 1.00
33.60 O
HETATM 7587 OA2 ATP 800 -7.501 2.503 -7.632 1.00
32.64 O
HETATM 7588 OA3 ATP 800 -6.483 4.274 -6.168 1.00
34.07 O
HETATM 7589 A5O ATP 800 -8.787 4.518 -6.833 1.00
36.40 O
HETATM 7590 A5C ATP 800 -8.403 5.464 -7.846 1.00
39.10 C
HETATM 7591 A4C ATP 800 -9.604 6.315 -8.269 1.00
41.61 C
HETATM 7592 A4O ATP 800
 60; -10.793 5.471 -8.462 1.00
42.22 O
HETATM 7593 A3C ATP 800 -9.937 7.303 -7.152 1.00
41.81 C
HETATM 7594 A3O ATP 800 -10.228 8.559 -7.756 1.00
43.61 O
HETATM 7595 A2C ATP 800 -11.191 6.724 -6.514 1.00
42.05 C
HETATM 

Re: [gmx-users] The energy minimization....

[MoJie Duan]

Hi, Mark:I have done the energy minimization and simulation of ATP in vacuum individual ( Maybe you have suggested me to do this yesterday, but actually I did not understand it, and just do this in solution).There are following problems:1. in the energy minimization, the potential energy is positive and in 14th step, it's potential energy is nan. But the .gro outfile of mdrun is just the same as the original file (i.e. the .gro file before minimization), the return messages of mdrun is (there are not any warning):--Getting Loaded...Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)Loaded with MoneyBack Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps =&
 #160; 200Step= 0, Dmax= 1.0e-02 nm, Epot= 1.06678e+05 Fmax= 3.63368e+06, atom= 26Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 3.63313e+06,  ^^^atom= 26Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax  1Double precision normally gives you higher accuracy.writing lowest energy coordinates.Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#Steepest Descents converged to machine precision in 15 steps,but did not reach the requested Fmax  1.Potential Energy = 1.0667836e+05Maximum for
 ce = 3.6336775e+06 on atom 26Norm of force = nan___2. in the full MD simulation, the warning coming, the messages is:Step 0, time 0 (ps) LINCS WARNINGrelative constraint deviation after LINCS:max 0.881911 (between atoms 27 and 28) rms nanbonds that rotated more than 30 degrees:atom 1 atom 2 angle previous, current, constraint length 27 28 90.0 0.1610 0.3030 0.1610Wrote pdb files with previous and current coordinatesstep 2490, remaining runtime: 0 s&
 #160; Writing final coordinates.Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#step 2500, remaining runtime: 0 s __And in the .gro file after this step, the coordinates of all atoms are nan. So it means there are crash in the structure? Is the crash between the atom 27 and 28? How to modify the structure file make it normal?Thank you very much!Duan<[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]>MoJie Duan wrote:   So look at your structures like I said last time! I'm not her
 e to give   my valuable time giving free advice in order to have it ignored...  Thank you very much for your kindness and patience. Maybe sometimes my   questions seems to be silly and boring, my knowledge about GROMACS is  really lack, sorry.  Actually, I really cannot understand what you said yesterday. Did you  mean is there any difference between the atom coordinates of ATP before-  and after- minimization? There would normally be some differences visible. If your topology was badly broken, then you would usually see where it was broken.  I found there are not any difference between  these two structure. (There are also not any obvious collision between atoms of ATP when  represent it by Rasmol) OK, so that means your structure is in a flat area of 
 the potential surface defined by your topology. If the topology is sound, then you're in business. My first recommendation was to minimize and/or equilibrate these structures on their own, and now I suggest doing them also in solvent. This will help you eliminate sources of problems and guide you to  what the real problem is. Divide and conquer... That's fine, then. OK, so here's your problem. Work out what's breaking and why. Read the error messages and look at the structures. Understand what each of  your .mdp file options does.Mark 

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Re: [gmx-users] The energy minimization....

[TJ Piggot]

Hi you need to explain in detail what steps you are doing before the 
minimisation and also what parameters you are using in your .mdp file 
because i have just run a minimisation of ATP (in water) to test the 
topology in the GROMOS96 ff and it works fine for me, so there must be a 
problem in one of your setup steps or your simulation parameters.


Tom

--On Friday, August 17, 2007 18:15:40 +0800 MoJie Duan 
[EMAIL PROTECTED] wrote:



Hi, Mark:
I have done the energy minimization and simulation of ATP in vacuum
individual ( Maybe you have suggested me to do this yesterday, but
actually I did not understand it, and just do this in solution).
There are following problems:
1. in the energy minimization, the potential energy is positive and in
14th step, it's potential energy is nan. But the .gro outfile of
mdrun is just the same as the original file (i.e. the .gro file before
minimization), the return messages of mdrun is (there are not any
warning):

--
Getting Loaded...
Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)
Loaded with Money


Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps    =  #160;    200
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.06678e+05 Fmax= 3.63368e+06, atom=
26
Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 3.63313e+06,
 ^^^
atom= 26
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  1

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  1.
Potential Energy  =  1.0667836e+05
Maximum for ce =  3.6336775e+06 on atom 26
Norm of force =    nan
___

2. in the full MD simulation, the warning coming, the messages is:


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.881911 (between atoms 27 and 28) rms nan
bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length
 27 28   90.0    0.1610   0.3030  0.1610
Wrote pdb files with previous and current coordinates
step 2490, remaining runtime: 0 s    #160;   Writing final
coordinates.

Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#
step 2500, remaining runtime: 0 s  
__

And in the .gro file after this step, the coordinates of all atoms are
nan. So it means there are crash in the structure? Is the crash between
the atom 27 and 28? How to modify the structure file make it normal?
Thank you very much!

Duan



MoJie Duan wrote:
  So look at your structures like I said last time! I'm not her e to
  give my valuable time giving free advice in order to have it
  ignored...
 Thank you very much for your kindness and patience. Maybe sometimes my
 questions seems to be silly and boring, my knowledge about GROMACS is
 really lack, sorry.

 Actually, I really cannot understand what you said yesterday. Did you
 mean is there any difference between the atom coordinates of ATP
 before-  and after- minimization?




There would normally be some differences visible. If your topology was
badly broken, then you would usually see where it was broken.



 I found there are not any difference between
 these two structure.
 (There are also not any obvious collision between atoms of ATP when
 represent it by Rasmol)



OK, so that means your structure is in a flat area of the potential
surface defined by your topology. If the topology is sound, then you're
in business.



My first recommendation was to minimize and/or equilibrate these
structures on their own, and now I suggest doing them also in solvent.
This will help you eliminate sources of problems and guide you to
what the real problem is. Divide and conquer...



That's fine, then.



OK, so here's your problem. Work out what's breaking and why. Read the
error messages and look at the structures. Understand what each of  
your .mdp file options does.


Mark






--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.

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Re: [gmx-users] The energy minimization....

[Alan Dodd]

The end structure is the same as the start because gromacs cannot find a lower 
energy structure than the initial one.  This indicates something severely 
wrong, either with the topology or starting structure.  You could get a better 
idea of what's going on by telling gromacs to output structures every step in 
the minimisation, and examining these so you can actually observe what is 
happening to your ATP.
I've occasionally seen similar results from minimisation, but only after doing 
something REALLY bad, like precisely overlaying two molecules on the same 
coordinates.  Debugging something like this is probably something only you are 
going to be able to do, as there are just so many potential ways a suitably, 
uh, imaginative user can mess things up.  

- Original Message 
From: MoJie Duan [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Sent: Friday, August 17, 2007 11:15:40 AM
Subject: Re: [gmx-users] The energy minimization

Hi, Mark:
I have done the energy minimization and simulation of ATP in vacuum individual 
( Maybe you have suggested me to do this yesterday, but actually I did not 
understand it, and just do this in solution).
There are following problems:
1. in the energy minimization, the potential energy is positive and in 14th 
step, it's potential energy is nan. But the .gro outfile of mdrun is just 
the same as the original file (i.e. the .gro file before minimization), the 
return messages of mdrun is (there are not any warning):

--
Getting Loaded...
Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)
Loaded with Money


Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps=  #160;200
Step=0, Dmax= 1.0e-02 nm, Epot=  1.06678e+05 Fmax= 3.63368e+06, atom= 26
Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 3.63313e+06, 
 ^^^
atom= 26
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  1

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  1.
Potential Energy  =  1.0667836e+05
Maximum for ce =  3.6336775e+06 on atom 26
Norm of force =nan
___

2. in the full MD simulation, the warning coming, the messages is:


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.881911 (between atoms 27 and 28) rms nan
bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length
 27 28   90.00.1610   0.3030  0.1610
Wrote pdb files with previous and current coordinates
step 2490, remaining runtime: 0 s#160;   Writing final 
coordinates.

Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#
step 2500, remaining runtime: 0 s   
__

And in the .gro file after this step, the coordinates of all atoms are nan. 
So it means there are crash in the structure? Is the crash between the atom 27 
and 28? How to modify the structure file make it normal?
Thank you very much!

Duan


MoJie Duan wrote:
  So look at your structures like I said last time! I'm not her e to give
  my valuable time giving free advice in order to have it ignored...
  Thank you very much for your kindness and patience. Maybe sometimes my 
  questions seems to be silly and boring, my knowledge about GROMACS is 
 really lack, sorry.
 
 Actually, I really cannot understand what you said yesterday. Did you 
 mean is there any difference between the atom coordinates of ATP before- 
 and after- minimization?


 There would normally be some differences visible. If your topology was
 badly broken, then you would usually see where it was broken.

 I found there are not any difference between 
 these two structure.
 (There are also not any obvious collision between atoms of ATP when 
 represent it by Rasmol)

 OK, so that means your structure is in a flat area of the potential
 surface defined by your topology. If the topology is sound, then you're
 in business.

 My first recommendation was to minimize and/or equilibrate these
 structures on their own, and now I suggest doing them also in solvent.
 This will help you eliminate sources of problems and guide you to 
 what the real problem is. Divide and conquer...

 That's fine, then.

 OK, so here's your problem. Work out what's breaking and why. Read the
 error messages and look at the structures. Understand what each of   your 
 .mdp file options does.

Mark

[gmx-users] Re: \[gmx\-users\] The energy minimization\.\.\.\. (fwd)

[TJ Piggot]

Hi

Also please keep emails on the list, it helps everyone (you getting more 
people's opinion than just mine, and people who may have a similar problem 
in the future)


Tom

 Forwarded Message 
Date: 18 August 2007 02:29 +0100
From: TJ Piggot [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: Re: \[gmx\-users\] The energy minimization\.\.\.\.

Hi

I just quickly checked and your ATP pdb file works fine for me (it did have
some weird characters in it that i had to delete, not sure if this was
caused by pasting it into an email). I should point out that this pdb file
is incomplete as you are missing some hydrogen atoms (pdb2gmx should tell
you this if you modified your .rtp file correctly). See any of the GROMOS96
.rtp file ATP entries for the hydrogens you have missed that still are
included in a united atom ff.

Also your .mdp parameters work fine with your pdb file so i have no idea
what is going wrong when you try! Check you have modified the .rtp file
correctly and are supplying sensible commands to
pdb2gmx/editconf/grompp/mdrun are the last things i can suggest.

Good luck

Tom

--On 18 August 2007 08:17 +0800 MoJie Duan [EMAIL PROTECTED] wrote:


Hi,Tom:
Thank you for your reply!
Before the minimization, I just change the atoms name of ATP, so it can
coordinated to the names in ffG43b1 (the atoms name of ATP in ffG43b1
also changed, each atom have a three-letter name).

My coordinate file (.pdb) was obtained from RCSB PDB, I extracted the xyz
coordinates of ATP molecule from the a .pdb file of a protein, as
following:
___
HETATM 7577  PG  ATP   800  -4.997   4.425  -2.604  1.00
33.08   P 
HETATM 7578  O1G ATP   800  -5.685   5.603  -1.764  1.00
33.76   O 
HETATM 7579  O2G ATP   800  -3.427   4.765  -2.665  1.00 32.63  
0;    O 
HETATM 7580  O3G ATP   800  -5.273   3.100  -1.967  1.00
33.16   O 
HETATM 7581  PB  ATP   800  -5.173   3.787  -5.388  1.00
34.37   P 
HETATM 7582  O1B ATP   800  -3.985   4.318  -6.120  1.00
33.33   O 
HETATM 7583  O2B ATP   800  -5.232   2.335  -5.045  1.00
33.33   O 
HETATM 7584  O3B ATP   800  -5.529   4.675  -4.089  1.00
33.22   O 
HETATM 7585  PA  ATP   800  -7.773   3.348  -6.436  1.00
35.04   P 
HETATM 7586  O1A ATP   800  -8.260   2.720  -5.177  1.00
33.60   O 
HETATM 7587  O2A ATP   800  -7.501   2.503  -7.632  1.00
32.64   O 
HETATM 7588  O3A ATP   800  -6.483   4.274  -6.168  1.00
34.07   O 
HETATM 7589  O5' ATP   800  -8.787   4.518 0; -6.833  1.00
36.40   O 
HETATM 7590  C5' ATP   800  -8.403   5.464  -7.846  1.00
39.10   C 
HETATM 7591  C4' ATP   800  -9.604   6.315  -8.269  1.00
41.61   C 
HETATM 7592  O4' ATP   800 -10.793   5.471  -8.462  1.00
42.22   O 
HETATM 7593  C3' ATP   800  -9.937   7.303  -7.152  1.00
41.81   C 
HETATM 7594  O3' ATP   800 -10.228   8.5 59  -7.756  1.00
43.61   O 
HETATM 7595  C2' ATP   800 -11.191   6.724  -6.514  1.00
42.05   C 
HETATM 7596  O2' ATP   800 -12.023   7.764  -6.036  1.00
41.49   O 
HETATM 7597  C1' ATP   800 -11.875   6.025  -7.679  1.00
42.90   C 
HETATM 7598  N9  ATP   800 -12.608   4.832  -7.218  1.00
43.53   N 
HETATM 7599  C8  ATP   800 -12.077   3. 810  -6.547  1.00
43.35   C 
HETATM 7600  N7  ATP   800 -13.023   2.904  -6.309  1.00
44.02   N 
HETATM 7601  C5  ATP   800 -14.162   3.341  -6.835  1.00
44.22   C 
HETATM 7602  C6  ATP   800 -15.461   2.828  -6.899  1.00
44.02   C 
HETATM 7603  N6  ATP   800 -15.751   1.647  -6.351  1.00
43.35   N 
HETATM 7604  N1  ATP   800 -16.41 4   3.547  -7.525  1.00
43.25   N 
HETATM 7605  C2  ATP   800 -16.125   4.717  -8.076  1.00
43.37   C 
HETATM 7606  N3  ATP   800 -14.902   5.230  -8.032  1.00
43.76   N 
HETATM 7607  C4  ATP   800 -13.901   4.571  -7.417  1.00
44.09   C


and then changed the atoms name:


HETATM 7577  APG ATP   800  -4.997   4.425  -2.604 #160; 1.00
33.08   P 
HETATM 7578  OG1 ATP   800  -5.685   5.603  -1.764  1.00
33.76   O 
HETATM 7579  OG2 ATP   800  -3.427   4.765  -2.665  1.00
32.63   O 
HETATM 7580  OG3 ATP   800  -5.273   3.100  -1.967  1.00
33.16   O 
HETATM 7581  APB ATP   800  -5.173   3.787  -5.388  1.00
34.37   P 
HETATM 7582  OB1 ATP   800  -3.985   4.3 18  -6.120  1.00
33.33   O 
HETATM 7583  OB2 ATP   800  -5.232   2.335  -5.045  1.00
33.33   O 
HETATM 7584  OB3 ATP   800  -5.529   4.675  -4.089  1.00
33.22   O 
HETATM 7585  APA ATP   800  -7.773   3.348  -6.436  1.00
35.04   P 
HETATM 7586  OA1 ATP   800  -8.260

Re: [gmx-users] The energy minimization....

[Tsjerk Wassenaar]

Hi,

Well, think harder about your 'problem'. How hard can it be to solve
all terms to reach the nearest local minimum for a system of 36 atoms?
You could basically do it by hand! No wonder that you reach
convergence to machine precision in 14 steps. Check the archives on
'stepsize too small' and 'convergence to machine precision', etc.

Cheers,

Tsjerk

On 8/16/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
 http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html



 Mark:
 I am sorry to disturb you. I'm a beginner of GROMACS and this mailing-list
 system. I even don't know how to replay a post directly. And yesterday I
 haven't seen your replay because the list title changed, sorry again!

 About the problem, I haven't resolved it yet. The .top file of my ATP
 molecule is generated by the pdb2gmx, and the coordinates of each atom
 adopted to the pdb file. The force file is ffG43a2. Whether my topology file
 of ATP molecule have something wrong? The topology file of ATP as following:

 ;File '../ATP/ATP.top' was generated
 ;By user: root (0)
 ;On host: mjduan-desktop
 ;At date: Wed Aug 15 16:55:53 2007
 ;
 ;This is your topology file
 ;Does All This Money Really Have To Go To Char ity ? (Rick)
 ;
 ; Include forcefield parameters
 #include ffG43a2.itp

 [ moleculetype ]
 ; Namenrexcl
 Protein 3

 [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
  chargeB  massB
  1 NR  1ATPAN9  1   -0.214.0067   ; qtot
 -0.2
  2  C  1 #1 60;  ATPAC4  10.2 12.011
 ; qtot 0
  3 NR  1ATPAN3  2  -0.3614.0067   ; qtot
 -0.36
  4CR1  1ATPAC2  2   0.36 13.019   ; qtot
 0
  5 NR  1ATPAN1  3  -0.3614.0067   ; qtot
 -0.36
  6  C  1ATPAC6  3   0.36 12.011   ; qtot
 0
  7 NT  1ATPAN6  4  -0.8314.0067   ; qtot
 -0.83
  8  H  1ATP   AH61  4  0.415  1.008   ; qtot
 -0.415
  9  H  1# 160;   ATP   AH62  4  0.415  1.008
 ; qtot 0
 10  C  1ATPAC5  5  0 12.011   ; qtot
 0
 11 NR  1ATPAN7  5  -0.3614.0067   ; qtot
 -0.36
 12CR1  1ATPAC8  5   0.36 13.019# 160;
 ; qtot 0
 13CH1  1ATP   AC1*  60.2 13.019   ; qtot
 0.2
 14 OA  1ATP   AO4*  6  -0.3615.9994   ; qtot
 -0.16
 15CH1  1ATP   AC4*  6   0.16 13.019   ; qtot
 0
 16CH1  1ATP   AC2*   #160;   7   0.15 13.019
 ; qtot 0.15
 17 OA  1ATP   AO2*  7 -0.54815.9994   ; qtot
 -0.398
 18  H  1ATP   AH2*  7  0.398  1.008   ; qtot
 0
 19CH1  1ATP   AC3*  8   0.15 13.019   ; qtot
 0.15
 20 # 160;   OA  1ATP   AO3*  8 -0.54815.9994
 ; qtot -0.398
 21  H  1ATP   AH3*  8  0.398  1.008   ; qtot
 0
 22CH2  1ATP   AC5*  9  0 14.027   ; qtot
 0
 23 OA  1ATP   AO5* 10  -0.36 #1 60;  15.9994
 ; qtot -0.36
 24  P  1ATPAPA 10  0.70530.9738   ; qtot
 0.345
 25 OM  1ATP   O1PA 10 -0.63515.9994   ; qtot
 -0.29
 26 OM  1ATP   O2PA 10 -0.63515.9994   ; qtot
 -0.925
 27 OA  1ATP   O3PA # 160;   11  -0.3615.9994
 ; qtot -1.285
 28  P  1ATPAPB 11  0.70530.9738   ; qtot
 -0.58
 29 OM  1ATP   O1PB 11 -0.63515.9994   ; qtot
 -1.215
 30 OM  1ATP   O2PB 11 -0.63515.9994   ; qtot
 -1.85
 31 OA  # 160;   1ATP   O3PB 12  -0.3615.9994
 ; qtot -2.21
 32  P  1ATPAPG 12   0.6330.9738   ; qtot
 -1.58
 33 OM  1ATP   O1PG 12 -0.63515.9994   ; qtot
 -2.215
 34 OM  1ATP   O2PG 12 -0.63515.9994   ; qtot
 -2.85
   #160 ; 35 OA  1ATP   O3PG 12 -0.54815.9994
 ; qtot -3.398
 36  H  1ATP   H3PG 12  0.398  1.008   ; qtot
 -3

 [ bonds ]
 ;  aiaj functc0c1c2c3
 1 2 2gb_9
 1 #160 ;  12 2gb_9
 113 2gb_21
 2 3 2gb_11
 210 2gb_15
 3 4 2gb_6
 4 5 2gb_6
 5 6 2gb_11
 6 7 2gb_8
 610 2gb_15
 7 8 2gb_2
 7#160 ;9 2gb_2
1011 2gb_9
1112  

Re: [gmx-users] The energy minimization....

[Mark Abraham]

[EMAIL PROTECTED] wrote:
 http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html
 
 
 
 Mark:
 I am sorry to disturb you. I'm a beginner of GROMACS and this 
 mailing-list system. I even don't know how to replay a post directly. 
 And yesterday I haven't seen your replay because the list title changed, 
 sorry again!

To reply to a list email, just reply as you would to any other email.

 About the problem, I haven't resolved it yet. The .top file of my ATP 
 molecule is generated by the pdb2gmx, and the coordinates of each atom 
 adopted to the pdb file. The force file is ffG43a2. Whether my topology 
 file of ATP molecule have something wrong? The topology file of ATP as 
 following:

The .top succeeded in minimizing the solvated structure, so that's a
good start. I think I can see that I was being too subtle for you
earlier with my suggestion that you think about observables that would
tell you whether your topology was working. Have you looked at the
before- and after-minimization structures to see whether they make sense
according to your training at recognizing chemical structures that will
be energy minima? If all of your components look reasonable
post-minimization on their own, and there were no significant warnings
or errors from grompp then your topologies probably are OK too. Then you
should go back and approach your original problem of getting a working
topology for your combination system.

Mark
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Re: [gmx-users] The energy minimization....

[Sampo Karkola]

Hi,

I struggled with a similar minimisation problem with NADP (NDPP topology
in ffG43a1). Then I got a suggestion from a colleague in Prof. Holtje's
group in Dusseldorf, that the atom naming should be changed from eg.
AC5* to something with only three characters, eg. C10. I renamed (and
only renamed) all the atoms with a unique running number and got rid of
the problem. I'm not sure if this will help you but it worked for me.

Hope it helps,

Sampo

[EMAIL PROTECTED] wrote:
 http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html
 
 
 
 Mark:
 I am sorry to disturb you. I'm a beginner of GROMACS and this 
 mailing-list system. I even don't know how to replay a post directly. 
 And yesterday I haven't seen your replay because the list title changed, 
 sorry again!
 
 About the problem, I haven't resolved it yet. The .top file of my ATP 
 molecule is generated by the pdb2gmx, and the coordinates of each atom 
 adopted to the pdb file. The force file is ffG43a2. Whether my topology 
 file of ATP molecule have something wrong? The topology file of ATP as 
 following:
 
 ;File '../ATP/ATP.top' was generated
 ;By user: root (0)
 ;On host: mjduan-desktop
 ;At date: Wed Aug 15 16:55:53 2007
 ;
 ;This is your topology file
 ;Does All This Money Really Have To Go To Char ity ? (Rick)
 ;
 ; Include forcefield parameters
 #include ffG43a2.itp
 
 [ moleculetype ]
 ; Namenrexcl
 Protein 3
 
 [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass  
 typeBchargeB  massB
  1 NR  1ATPAN9  1   -0.214.0067   ; 
 qtot -0.2
  2  C  1 
 60;  ATPAC4  10.2 
 12.011   ; qtot 0
  3 NR  1ATPAN3  2  -0.3614.0067   ; 
 qtot -0.36
  4CR1  1ATPAC2  2   0.36 13.019   ; 
 qtot 0
  5 NR  1ATPAN1  3  -0.3614.0067   ; 
 qtot -0.36
  6  C  1ATPAC6  3   0.36 12.011   ; 
 qtot 0
  7 NT  1ATPAN6  4  -0.8314.0067   ; 
 qtot -0.83
  8  H  1ATP   AH61  4  0.415  1.008   ; 
 qtot -0.415
  9  H  1# 160;   ATP   AH62  4  0.415  
 1.008   ; qtot 0
 10  C  1ATPAC5  5  0 12.011   ; 
 qtot 0
 11 NR  1ATPAN7  5  -0.3614.0067   ; 
 qtot -0.36
 12CR1  1ATPAC8  5   0.36 13.019# 
 160;  ; qtot 0
 13CH1  1ATP   AC1*  60.2 13.019   ; 
 qtot 0.2
 14 OA  1ATP   AO4*  6  -0.3615.9994   ; 
 qtot -0.16
 15CH1  1ATP   AC4*  6   0.16 13.019   ; 
 qtot 0
 16CH1  1ATP   AC2*   #160;   7   0.15 
 13.019   ; qtot 0.15
 17 OA  1ATP   AO2*  7 -0.54815.9994   ; 
 qtot -0.398
 18  H  1ATP   AH2*  7  0.398  1.008   ; 
 qtot 0
 19CH1  1ATP   AC3*  8   0.15 13.019   ; 
 qtot 0.15
 20 # 160;   OA  1ATP   AO3*  8 -0.548
 15.9994   ; qtot -0.398
 21  H  1ATP   AH3*  8  0.398  1.008   ; 
 qtot 0
 22CH2  1ATP   AC5*  9  0 14.027   ; 
 qtot 0
 23 OA  1ATP   AO5* 10  -0.36 
 60;  
 15.9994   ; qtot -0.36
 24  P  1ATPAPA 10  0.70530.9738   ; 
 qtot 0.345
 25 OM  1ATP   O1PA 10 -0.63515.9994   ; 
 qtot -0.29
 26 OM  1ATP   O2PA 10 -0.63515.9994   ; 
 qtot -0.925
 27 OA  1ATP   O3PA # 160;   11  -0.36
 15.9994   ; qtot -1.285
 28  P  1ATPAPB 11  0.70530.9738   ; 
 qtot -0.58
 29 OM  1ATP   O1PB 11 -0.63515.9994   ; 
 qtot -1.215
 30 OM  1ATP   O2PB 11 -0.63515.9994   ; 
 qtot -1.85
 31 OA  # 160;   1ATP   O3PB 12  -0.36
 15.9994   ; qtot -2.21
 32  P  1ATPAPG 12   0.6330.9738   ; 
 qtot -1.58
 33 OM  1ATP   O1PG 12 -0.63515.9994   ; 
 qtot -2.215
 34 OM  1ATP   O2PG 12 -0.63515.9994   ; 
 qtot -2.85
 ; 35 OA  1ATP   O3PG 12 -0.54815.9994   
 ; qtot -3.398
 36  H  1ATP   H3PG 12  0.398  1.008   ; 
 qtot -3
 
 [ bonds ]
 ;  aiaj functc0c1c2c3
 1 2 2gb_9
 1   ;  12 2gb_9
 113 2gb_21
 2 3 2gb_11
 210 2gb_15
 3 4 2gb_6
 4 5 2gb_6
 5 6 2gb_11
 6 7 2

Re: [gmx-users] The energy minimization....

[Justin A. Lemkul]

Quoting [EMAIL PROTECTED]:

 Hi, everyone:
 I have meet some problem when simulating a protein and ATP complex. The
 energy minimization will stop after 14 steps. I had followed Mark's
 suggestion, did the protein and ATP eneryg minimization independently,
 and#160; found that the protein can finish its minimization correctly,
 but#160; the#160; ATP 's minimization stopped after 14 steps. So it seems
 that there are something wrong with ATP. And Mark also said Probably your
 topology is broken, what is it means? What should I do now?
 Best wishes!






==

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

==
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Re: [gmx-users] The energy minimization....

[MoJie Duan]

   Mark:Thank you for your reply!I have checked my topology file of the ATP, I think there isn't any problem with it. When I do the grompp (only use the ATP molecule), there is not any warning and error, it stopped at 14th step, and return the following messege:Step= 0, Dmax= 1.0e-02 nm, Epot= -1.88000e+04 Fmax= 1.71469e+04, atom= 421Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 1.59347e+04, atom= 4214Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax  1it's really strange for Epot = nan. I think maybe there are something wrong with it even it said Converged to machine precision.But when I do the full MD Simulation (not energy minimization), the program said Fatal error:Number of grid cells is zero. Probably the system and box collapse
 d!!! (there also isnot any warning and error in grompp). I think the problem maybe caused by the energy minimization step, but I really don't know why!Duan[EMAIL PROTECTED] wrote:To reply to a list email, just reply as you would to any other email.The .top succeeded in minimizing the solvated structure, so that's agood start. I think I can see that I was being too subtle for youearlier with my suggestion that you think about observables that wouldtell you whether your topology was working. Have you looked at thebefore- and after-minimization structures to see whether they make sense according to your training at recognizing chemical structures that will be energy minima? If all of your components look reasonablepost-minimization on their own, and there were no significant warningsor errors from grompp then your topolog
 ies probably are OK too. Then you should go back and approach your original problem of getting a working topology for your combination system.Mark  

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Re: [gmx-users] The energy minimization....

[Mark Abraham]

MoJie Duan wrote:
 Mark:
 Thank you for your reply!
 I have checked my topology file of the ATP, I think there isn't any 
 problem with it. When I do the grompp (only use the ATP molecule), there 
 is not any warning and error, it stopped at 14th step, and return the 
 following messege:
 
 Step=0, Dmax= 1.0e-02 nm, Epot= -1.88000e+04 Fmax= 1.71469e+04, 
 atom= 421
 Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 1.59347e+04, 
 atom= 4214
 Stepsize too small, or no change in energy.
 Converged to machine precision,
 but not to the requested precision Fmax  1
 
 it's really strange for Epot = nan. I think maybe there are something 
 wrong with it even it said Converged to machine precision.
 But when I do the full MD Simulation (not energy minimization), the 
 program said Fatal error:Number of grid cells is zero. Probably the 
 system and box collapse d!!! (there also isnot any warning and error in 
 grompp). I think the problem maybe caused by the energy minimization 
 step, but I really don't know why!

So look at your structures like I said last time! I'm not here to give
my valuable time giving free advice in order to have it ignored...

  [EMAIL PROTECTED] wrote:
 
  To reply to a list email, just reply as you would to any other email.
 
 
  The .top succeeded in minimizing the solvated structure, so that's a
  good start. I think I can see that I was being too subtle for you
  earlier with my suggestion that you think about observables that would
  tell you whether your topology was working. Have you looked at the
  before- and after-minimization structures to see whether they make 
  sense according to your training at recognizing chemical structures 
  that will be energy minima? If all of your components look reasonable
  post-minimization on their own, and there were no significant warnings
  or errors from grompp then your topolog ies probably are OK too. Then 
  you should go back and approach your original problem of getting a 
  working topology for your combination system.
 
  Mark
 
 
 
 
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Re: [gmx-users] The energy minimization....

[MoJie Duan]

<[EMAIL PROTECTED]><[EMAIL PROTECTED]>So look at your structures like I said last time! I'm not here to givemy valuable time giving free advice in order to have it ignored...Thank you very much for your kindness and patience. Maybe sometimes my questions seems to be silly and boring, my knowledge about GROMACS is really lack, sorry.Actually, I really cannot understand what you said yesterday. Did you mean is there any difference between the atom coordinates of ATP before- and after- minimization? I found there are not any difference between these two structure.(There are also not any obvious collision between atoms of ATP when represent it by Rasmol)   [EMAIL PROTECTED] wrote:   To reply to a list email, just reply as you would to any other email.The .top succeeded in minimizing the solvated structure, so 
 that's a  good start. I think I can see that I was being too subtle for you  earlier with my suggestion that you think about observables that would  tell you whether your topology was working. Have you looked at the  before- and after-minimization structures to see whether they make   sense according to your training at recognizing chemical structures   that will be energy minima? If all of your components look reasonable post-minimization on their own, what means?  and there were no significant warnings  or errors from grompp then your topolog ies probably are OK too. ^just like I said in last email, there are not any warnning and error from grompp. Thenyou should go back and approach your original problem of gettingworking topology f
 or your combination system. I cannot run the full MD SImulation for ATP individually, so I think maybe there are something problem with it (I used the same minim.mdp can successfully do the energy minimization of the protein individually). I really confused.   Mark<[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]> 

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Re: [gmx-users] The energy minimization....

[Mark Abraham]

MoJie Duan wrote:
  So look at your structures like I said last time! I'm not here to give
  my valuable time giving free advice in order to have it ignored...
 
 Thank you very much for your kindness and patience. Maybe sometimes my 
 questions seems to be silly and boring, my knowledge about GROMACS is 
 really lack, sorry.
 
 Actually, I really cannot understand what you said yesterday. Did you 
 mean is there any difference between the atom coordinates of ATP before- 
 and after- minimization?


There would normally be some differences visible. If your topology was
badly broken, then you would usually see where it was broken.

  I found there are not any difference between 
 these two structure.
 (There are also not any obvious collision between atoms of ATP when 
 represent it by Rasmol)

OK, so that means your structure is in a flat area of the potential
surface defined by your topology. If the topology is sound, then you're
in business.

   [EMAIL PROTECTED] wrote:
  
   To reply to a list email, just reply as you would to any other email.
  
  
   The .top succeeded in minimizing the solvated structure, so that's a
   good start. I think I can see that I was being too subtle for you
   earlier with my suggestion that you think about observables that would
   tell you whether your topology was working. Have you looked at the
   before- and after-minimization structures to see whether they make
   sense according to your training at recognizing chemical structures
   that will be energy minima? If all of your components look 
 reasonable post-minimization on their own,
   what means?

My first recommendation was to minimize and/or equilibrate these
structures on their own, and now I suggest doing them also in solvent.
This will help you eliminate sources of problems and guide you to what
the real problem is. Divide and conquer...

and there were no significant warnings
   or errors from grompp then your topolog ies probably are OK too.
 ^just like I said in last email, there 
 are not any warnning and error from grompp.

That's fine, then.

   Thenyou should go back and approach your original problem of getting
   working topology f or your combination system.
 I cannot run the 
 full MD SImulation for ATP individually, so I think maybe there are 
 something problem with it (I used the same minim.mdp can successfully do 
 the energy minimization of the protein individually).  I really confused.

OK, so here's your problem. Work out what's breaking and why. Read the
error messages and look at the structures. Understand what each of your
.mdp file options does.

Mark
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Re: [gmx-users] The energy minimization....

[Mark Abraham]

 Hi, everyone:br /I have meet some problem when simulating a protein and
 ATP complex. The energy minimization will stop after 14 steps. I had
 followed Mark's suggestion, did the protein and ATP eneryg minimization
 independently, and#160; found that the protein can finish its
 minimization correctly, but#160; the#160; ATP 's minimization stopped
 after 14 steps. So it seems that there are something wrong with ATP. And
 Mark also said quot;Probably your topology is brokenquot;, what is it
 means? What should I do now?

If you're going to quote somebody from here
http://www.gromacs.org/pipermail/gmx-users/2007-August/029115.html, don't
imply that they made the comment in relation to another post entirely
(unless you're trying to annoy them, that is).

I replied to the above question on the list yesterday here
http://www.gromacs.org/pipermail/gmx-users/2007-August/029132.html

Mark

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Re: [gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

[Mark Abraham]

Arun kumar wrote:

Hi Tsjerk and others,
I tried to simulate one surfactant and one
chloride ion in 500 waters and got similar type of errors. I mean my
system got collapsed for l-bfgs minimization and for steepest descent
the potential energy is a large number.(obviously some bad contacts).
It seems the problem is with topology. Earlier I asked about what is
meant by broken topology?? Can anyone tell what may ne the problem and
also about what is meant by broken topology??


A broken topology is where you haven't managed to describe the bond 
connectivity in your .top file that you'd like to. The way to fix it is 
to reduce your problem to its simplest form (single surfactant in 
vacuum, as David suggests), observe where the breakage occurs, read 
chapter 5 carefully, and remedy appropriately.


Mark
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Re: [gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

[Arun kumar]

Hai Tsjerk, David, Mark and others,
  Thank you for all
your responses. I had been successful in setting up simulation and
also in understanding what David and Mark told. As Dr. David
suggested, I started EM for single surfactant in vaccum and successful
in minimizing the energy. Also I did EM for my co-surfactant stearyl
alcohol and had been successful. Then I started minimizing the energy
of a system of 500 waters+ 1 cationic surf+ 1 fatty alcohol. It also
worked fine.  And I started true dynamics(MD) of the bulk system and
had been successful. I think all these posts will be useful for others
who start gromacs with these kind of systems. So for me, Now the only
problem is getting correct forcefield for my surfactant system to get
good physical properties. I will post the topology for my surf and
co-surf when I will be successful in doing that.

Thanks and Regards
Arun Kumar

On 5/6/07, Mark Abraham [EMAIL PROTECTED] wrote:

Arun kumar wrote:
 Hi Tsjerk and others,
 I tried to simulate one surfactant and one
 chloride ion in 500 waters and got similar type of errors. I mean my
 system got collapsed for l-bfgs minimization and for steepest descent
 the potential energy is a large number.(obviously some bad contacts).
 It seems the problem is with topology. Earlier I asked about what is
 meant by broken topology?? Can anyone tell what may ne the problem and
 also about what is meant by broken topology??

A broken topology is where you haven't managed to describe the bond
connectivity in your .top file that you'd like to. The way to fix it is
to reduce your problem to its simplest form (single surfactant in
vacuum, as David suggests), observe where the breakage occurs, read
chapter 5 carefully, and remedy appropriately.

Mark
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--
Arun kumar.V
M.E Chemical
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Re: [gmx-users] Failed Energy Minimization

[Mark Abraham]

Justin M. Shorb wrote:

Greetings:

I have been having trouble running any energy minimization with any sort 
of system. I have small polypeptides in water, and then large proteins 
in water with the same error message:


No matter what run parameters I get, I always get ci = -2147483648. Even 
different systems. (This, I realize is simply numerically infinity). If 
I try running with ns_type = simple, the em runs until it hits around 35 
and then says it didn't converge. Since I am running grompp_d -v, I get 
that there are certain atoms that have infinite potential. But, 
depending on the system, the atom type (solvent or molecule) changes.


This suggests a problem with your force field and/or topology.

I have noted that previous posts have been answered with an admonition: 
Find out which atoms are infinite force, and then fix it. I suppose I 
could go through, find the atoms and remove those waters that overlap, 
but shouldn't this be taken into account by the genbox_d program? I also 
have tried to increase the vdw radii in the vdwradii.dat file to have it 
delete more waters. But, even after having 60 fewer waters around a 88 
kD protein, the system still fails to energy minimize.


This suggests that the source of the problem isn't that these atoms 
start life too close together, but maybe they're moving too close 
together because of some other problem? (Unless the error is always 
happening before the first EM step)


Given that this seems to be a common problem in solvating a system, are 
there better options (options for genbox??) than running the following 
shell commands? The em.mdp file is also shown below.


That all seems fine.

Mark
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Re: [gmx-users] Re: Energy Minimization nan WARNING 1 [file blah.itp, line 1020]: No default G96Angle types, using zeroes

[David van der Spoel]

Joern Lenz wrote:

On Wednesday 16 August 2006 16:32, you wrote:

dear gromacs users,
i am new to gromacs (using version 3.3.1) and trying to simulate an enzyme
which is covalently bound to a piece of dna i.e. a tyrosine is connected to
the dna backbone establishing a phosphodiester group.
but each time i try to start the simulation using the G43a1 forcefield
there occurs a warning like
WARNING 1 [file blah.itp, line 1020]:
No default G96Angle types, using zeroes
or
WARNING 39 [file blah.itp, line 1509]:
No default Proper Dih. types, using zeroes

i browsed to the mailing list archive and found lots of problems similar to
mine but - forgive me -  i am not able to fix my problem with these hints.
i know that i have to add these angles and dihedrals in the itp or rtp
files. But where exactly and how.

one example oif a missing angle is the connection from one nucleeotide to
the next in the DNA (O3* - P - O1P).
Can anyone tell me how to add the missing lines and where to do that
exactly (perhaps with a little example) ???
That would be of great help for me. Otherwise I will die unhappy ...

Another problem is: where to tell GROMACS that there is a connective bond,
angle, dihedral between an aminoacid (the phenolic group of tyrosine) and
the DNA backbone ?

So if you have any suggestions that could help me, be so kind and try to
answer my question.
Have a nice day
Joe

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first you probably need to use another force field like amber or opls 
since gromos is not very well suited for DNA.


you can define a special bond in the specbond.dat file. copy it to your 
working dir and edit it as appropriate.


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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