[gmx-users] remove the atom clashes-reg

[ITHAYARAJA]

Hi Dear,

I am doing simulation with three ligand so that I have applied deprecated
force field to the system.

I went through the reference which you cited to the following error. I
understood the error that It could be a clashes. It wanted to  remove atom
clashes from my coordinate file, so Is there any option to do the same. help
me.

Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype NR not found

-- 
**
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India
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[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)

[Krapnik]

Dear all,

We have tested more strange behavior of constraints from pull code for
calculation of free energy differences small molecule on DOPC membrane and
octanol slab.
As I have reported previously, while the errors in free energy differences
on DOPC were rather small, the errors on octanol were strangely high.

We have prepared smaller slabs (as Mark suggested) of octanol with
comparable size of box and we have also tried to analyze the position of
centres either via pullx.xvg provided by pull code, but also by g_dist
utility and to our surprise, size matters. A lot.
(Same groups were used in mdp for pull and for g_dist analysis, only
distances in z-axis is shown)

DOPC, 128 molecules, box size 6.2 6.4 8.3 , position of small molecule on
the edge of membrane
Time(ps)   pullf.xvgdist.xvg
  0.00-0.12416-0.12436
  1.00-0.12416-0.12433
  2.00-0.12416-0.12428
  3.00-0.12416-0.12430
  4.00-0.12416-0.12430
  5.00-0.12416-0.12432
  6.00-0.12416-0.12434
  7.00-0.12416-0.12449
As can be seen, the variation of distances reported by these two programs is
not perfect, but it is rather ok with precision of about 0.001 nm.

Octanol, 957 molecules, box size 5.7 5.9 13.7, position is similar on the
edge of slab, errors in free energy profiles are mainly here.
Time(ps)pullf.xvgdist.xvg
  0.00-2.81855-3.41133
  1.00-2.81076-3.44213
  2.00-2.82005-3.27949
  3.00-2.81856-3.35097
  4.00-2.82016-3.50378
  5.00-2.81849-3.63261
  6.00-2.81855-3.60058
  7.00-2.81870-3.80251
  8.00-2.81859-3.32790
  9.00-2.81849-3.24329
 10.00-2.81855-3.28394
 21.00-2.81855-4.02524
Here, the distances reported by pull code and by g_dist are completely
different with differences in about 1 nm! Visual inspection in VMD says that
small molecule is highly mobile a actual distances are reported rightly by
g_dist program.
Strangely enough, when we put distance measured by g_dist as a start into
the pull code without guessing the distances, but this also did not worked,
since the molecule tried to be at some completely different position and the
simulation crashed as the molecule speeded up.

Octanol, 475 molecules, box size 5.5 5.5 9.5, position also on the edge of
the slab
Time(ps)  pullf.xvgdist.xvg
  0.00-0.49996-0.49989
  1.00-0.49996-0.49988
  2.00-0.49996-0.49981
  3.00-0.49996-0.49981
  4.00-0.49996-0.50001
  5.00-0.49996-0.49987
  6.00-0.49996-0.49986
  7.00-0.49996-0.49994
  8.00-0.49997-0.49988
  9.00-0.49996-0.49980
 10.00-0.49996-0.49988
Smaller box cured miraculously the problem, since here the difference is
similarly small as in DOPC case.

However just to remind another ache we had with octanol slab, in case of
octanol, the size of box in xy plane had to be held constant as the box
narrowed thorough the whole simulation when in anisotropic NPT ensemble.

Why g_dist and pullx show so different results in large box, I still do not
understand. Any suggestions?
And possibly any suggestions whether our box narrowing in case of octanol is
common or do we have another devil hidden there?

Best wishes
-- 
Zdraví skoro zdravý
Karel "Krápník" Berka


RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
tel: +420-585634769
fax: +420-585634769
e-mail: karel.be...@upol.cz


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Re: [gmx-users] remove the atom clashes-reg

[Mark Abraham]

On 31/08/2011 6:15 PM, ITHAYARAJA wrote:

Hi Dear,

I am doing simulation with three ligand so that I have applied 
deprecated force field to the system.


That's a bad reason to choose a deprecated force field.

I went through the reference which you cited to the following error. I 
understood the error that It could be a clashes. It wanted to  remove 
atom clashes from my coordinate file, so Is there any option to do the 
same.


You need to design your coordinate file construction or system 
preparation protocol better. We can't help because we don't know what 
you're doing. Follow the links from the URL I gave last time. Read as 
much as you can. Describe as fully as you can when asking for help.



help me.

Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype NR not found


Whatever you did to your topology had nothing to do with helping resolve 
atomic clashes.


Mark
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[gmx-users] g_hbond

[Steven Neumann]

Hi Gromacs Users,

I have calculated hydrogen bonds and collisions between my ligands and every
single residue using g_hbond. Looking at the criteria adpoted by Gromacs I
found impossible that number of hydrogen bonds were higher than number of
collisions... And what is interesting in one of my residue I obtained result
like this... All Hbonds with Glycine - 1872, All Collisions 704.

Does anyone know how is it possible?

Steven
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Re: [gmx-users] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:

Hi Gromacs Users,
 
I have calculated hydrogen bonds and collisions between my ligands and 
every single residue using g_hbond. Looking at the criteria adpoted by 
Gromacs I found impossible that number of hydrogen bonds were higher 
than number of collisions... And what is interesting in one of my 
residue I obtained result like this... All Hbonds with Glycine - 1872, 
All Collisions 704.
 
Does anyone know how is it possible?
 


I don't know how any of your numbers are possible (1872 H-bonds forming with a 
glycine?), or what you are defining as a collision and how you calculated it. 
Please provide the exact commands that you're using.  If you're equating a 
contact (e.g. from g_mindist) with a collision, then realize that the default 
criteria for a contact are very different than the geometric criteria for a 
hydrogen bond.


-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] g_hbond

[Steven Neumann]

On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Hi Gromacs Users,
>>  I have calculated hydrogen bonds and collisions between my ligands and
>> every single residue using g_hbond. Looking at the criteria adpoted by
>> Gromacs I found impossible that number of hydrogen bonds were higher than
>> number of collisions... And what is interesting in one of my residue I
>> obtained result like this... All Hbonds with Glycine - 1872, All Collisions
>> 704.
>>  Does anyone know how is it possible?
>>
>>
>
> I don't know how any of your numbers are possible (1872 H-bonds forming
> with a glycine?), or what you are defining as a collision and how you
> calculated it. Please provide the exact commands that you're using.  If
> you're equating a contact (e.g. from g_mindist) with a collision, then
> realize that the default criteria for a contact are very different than the
> geometric criteria for a hydrogen bond.
>
> -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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>



My system is made of 10 ligands and one protein. I used command:

g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg

Where I specified in the index file two groups: 10 ligands and Glycine
residue. So I have calculated hbonds (second column) and collisions (third
column) and then I made a sum of all frames during 100 ns simualtion time
(one frame every 50 ps) obtaining 1872 hbonds and 703 collisions between
Glycine and 10 ligands. I did it with every residue to assess binding
affinity of different amino acids.
Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A and
angle. So when calcualting hbond and collisions the number of hbonds has has
to be smaller while collision takes into account hbonds as welll. I obtained
results like this for all other residues which seems to be correct. Am I
right?

Steven
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Re: [gmx-users] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:

Hi Gromacs Users,
 I have calculated hydrogen bonds and collisions between my
ligands and every single residue using g_hbond. Looking at the
criteria adpoted by Gromacs I found impossible that number of
hydrogen bonds were higher than number of collisions... And what
is interesting in one of my residue I obtained result like
this... All Hbonds with Glycine - 1872, All Collisions 704.
 Does anyone know how is it possible?
 



I don't know how any of your numbers are possible (1872 H-bonds
forming with a glycine?), or what you are defining as a collision
and how you calculated it. Please provide the exact commands that
you're using.  If you're equating a contact (e.g. from g_mindist)
with a collision, then realize that the default criteria for a
contact are very different than the geometric criteria for a
hydrogen bond.

-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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My system is made of 10 ligands and one protein. I used command:
 
g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
 
Where I specified in the index file two groups: 10 ligands and Glycine 
residue. So I have calculated hbonds (second column) and collisions 
(third column) and then I made a sum of all frames during 100 ns 
simualtion time (one frame every 50 ps) obtaining 1872 hbonds and 703 
collisions between Glycine and 10 ligands. I did it with every residue 
to assess binding affinity of different amino acids.
Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A 
and angle. So when calcualting hbond and collisions the number of hbonds 
has has to be smaller while collision takes into account hbonds as 
welll. I obtained results like this for all other residues which seems 
to be correct. Am I right? 
 


No.  The second column is not inclusive of the first.  It counts the number of 
atoms that are within hydrogen bonding distance, but do not meet the criteria 
because of the angle between D-H-A.


-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] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:

Hi Gromacs Users,
 I have calculated hydrogen bonds and collisions between my
ligands and every single residue using g_hbond. Looking at the
criteria adpoted by Gromacs I found impossible that number of
hydrogen bonds were higher than number of collisions... And what
is interesting in one of my residue I obtained result like
this... All Hbonds with Glycine - 1872, All Collisions 704.
 Does anyone know how is it possible?
 



I don't know how any of your numbers are possible (1872 H-bonds
forming with a glycine?), or what you are defining as a collision
and how you calculated it. Please provide the exact commands that
you're using.  If you're equating a contact (e.g. from g_mindist)
with a collision, then realize that the default criteria for a
contact are very different than the geometric criteria for a
hydrogen bond.

-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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My system is made of 10 ligands and one protein. I used command:
 
g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
 
Where I specified in the index file two groups: 10 ligands and Glycine 
residue. So I have calculated hbonds (second column) and collisions 
(third column) and then I made a sum of all frames during 100 ns 
simualtion time (one frame every 50 ps) obtaining 1872 hbonds and 703 
collisions between Glycine and 10 ligands. I did it with every residue 
to assess binding affinity of different amino acids.


I forgot to mention in the previous message that there is no value in summing 
the hydrogen bonds over time.  Some of those H-bonds may be distinct, and others 
may be the same H-bond that has broken and subsequently re-formed.  I doubt 
anyone would find real value in saying that 10 ligands formed 1872 H-bonds with 
glycine over a trajectory.


-Justin

Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A 
and angle. So when calcualting hbond and collisions the number of hbonds 
has has to be smaller while collision takes into account hbonds as 
welll. I obtained results like this for all other residues which seems 
to be correct. Am I right? 
 
Steven




--


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] g_hbond

[Steven Neumann]

On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>>
>>
>> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Steven Neumann wrote:
>>
>>Hi Gromacs Users,
>> I have calculated hydrogen bonds and collisions between my
>>ligands and every single residue using g_hbond. Looking at the
>>criteria adpoted by Gromacs I found impossible that number of
>>hydrogen bonds were higher than number of collisions... And what
>>is interesting in one of my residue I obtained result like
>>this... All Hbonds with Glycine - 1872, All Collisions 704.
>> Does anyone know how is it possible?
>>
>>
>>I don't know how any of your numbers are possible (1872 H-bonds
>>forming with a glycine?), or what you are defining as a collision
>>and how you calculated it. Please provide the exact commands that
>>you're using.  If you're equating a contact (e.g. from g_mindist)
>>with a collision, then realize that the default criteria for a
>>contact are very different than the geometric criteria for a
>>hydrogen bond.
>>
>>-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
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
>>
>> >
>> before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>
>>Can't post? Read 
>> http://www.gromacs.org/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>  My system is made of 10 ligands and one protein. I used command:
>>  g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
>>  Where I specified in the index file two groups: 10 ligands and Glycine
>> residue. So I have calculated hbonds (second column) and collisions (third
>> column) and then I made a sum of all frames during 100 ns simualtion time
>> (one frame every 50 ps) obtaining 1872 hbonds and 703 collisions between
>> Glycine and 10 ligands. I did it with every residue to assess binding
>> affinity of different amino acids.
>>
>
> I forgot to mention in the previous message that there is no value in
> summing the hydrogen bonds over time.  Some of those H-bonds may be
> distinct, and others may be the same H-bond that has broken and subsequently
> re-formed.  I doubt anyone would find real value in saying that 10 ligands
> formed 1872 H-bonds with glycine over a trajectory.
>
> -Justin
>
> Obviosuly, but it can provide you some information about binding affinity -
some ligands remains close to some residues longer than the others so by sum
of this values you can assess residues with higher binding affinity.

Steven

>
> Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A and
>> angle. So when calcualting hbond and collisions the number of hbonds has has
>> to be smaller while collision takes into account hbonds as welll. I obtained
>> results like this for all other residues which seems to be correct. Am I
>> right?  Steven
>>
>>
>  --
> ==**==
>
> 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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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
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[gmx-users] pdb2gmx of nucleic acids with ffamber03 force field

[MARIA ICIAR FRADES ALZUETA]

Dear all,

I am trying to pdb2gmx a a pdb file gcaa.pdb having nucleic acids  
using amber force field 03:

pdb2gmx -ff amber03 -f gcaa.pdb -o rna.pdb -p rna.top -water tip3p

I have two questions:
1.
The ffamber03.rtp file specifies that O2 from should be O to be  
recognized by the rtp file. When one substitutes this atom the program  
complains:

Fatal error:
Atom O in residue RC 4 was not found in rtp entry RC with 31 atoms
while sorting atoms.

Keeping the original pdb O2 works fine, althought O2 is not in the  
ffamber03.rtp  file. Is this fine?


2.
When doing: editconf -f gcaa.pdb -o this.pdb
The residues named H2'1 as mapped in the .rtp file they became 1H2'.  
The pdb2gmx works fine but I do not know how it works if the new 1H2'  
is not in the ffamber03.rtp file.


Thanks!
Regards,
Itziar Frades


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Re: [gmx-users] g_hbond

[Steven Neumann]

On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>>
>>
>> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Steven Neumann wrote:
>>
>>Hi Gromacs Users,
>> I have calculated hydrogen bonds and collisions between my
>>ligands and every single residue using g_hbond. Looking at the
>>criteria adpoted by Gromacs I found impossible that number of
>>hydrogen bonds were higher than number of collisions... And what
>>is interesting in one of my residue I obtained result like
>>this... All Hbonds with Glycine - 1872, All Collisions 704.
>> Does anyone know how is it possible?
>>
>>
>>I don't know how any of your numbers are possible (1872 H-bonds
>>forming with a glycine?), or what you are defining as a collision
>>and how you calculated it. Please provide the exact commands that
>>you're using.  If you're equating a contact (e.g. from g_mindist)
>>with a collision, then realize that the default criteria for a
>>contact are very different than the geometric criteria for a
>>hydrogen bond.
>>
>>-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
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
>>
>> >
>> before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>
>>Can't post? Read 
>> http://www.gromacs.org/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>  My system is made of 10 ligands and one protein. I used command:
>>  g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
>>  Where I specified in the index file two groups: 10 ligands and Glycine
>> residue. So I have calculated hbonds (second column) and collisions (third
>> column) and then I made a sum of all frames during 100 ns simualtion time
>> (one frame every 50 ps) obtaining 1872 hbonds and 703 collisions between
>> Glycine and 10 ligands. I did it with every residue to assess binding
>> affinity of different amino acids.
>> Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A
>> and angle. So when calcualting hbond and collisions the number of hbonds has
>> has to be smaller while collision takes into account hbonds as welll. I
>> obtained results like this for all other residues which seems to be correct.
>> Am I right?
>>
>
> No.  The second column is not inclusive of the first.  It counts the number
> of atoms that are within hydrogen bonding distance, but do not meet the
> criteria because of the angle between D-H-A.
>
>
> -Justin
>
> In this case number of collisions has to include number of hbonds. If
> collision is counted as a distance <3.5 and hbond distance <3.5 plus angle
> D-H-A means that collisions covers hbonds... Explain please whether I am
> wrong.
>




>  ==**==
>
> 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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> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or se

Re: [gmx-users] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:



On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Steven Neumann wrote:

   Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my
   ligands and every single residue using g_hbond. Looking
at the
   criteria adpoted by Gromacs I found impossible that number of
   hydrogen bonds were higher than number of collisions...
And what
   is interesting in one of my residue I obtained result like
   this... All Hbonds with Glycine - 1872, All Collisions 704.
Does anyone know how is it possible?
   


   I don't know how any of your numbers are possible (1872 H-bonds
   forming with a glycine?), or what you are defining as a collision
   and how you calculated it. Please provide the exact commands that
   you're using.  If you're equating a contact (e.g. from g_mindist)
   with a collision, then realize that the default criteria for a
   contact are very different than the geometric criteria for a
   hydrogen bond.

   -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

   >

   ====
   -- gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users

   >
   Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/Search

   > before
posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to gmx-users-requ...@gromacs.org

   >.

   Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists

   >


 My system is made of 10 ligands and one protein. I used command:
 g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
 Where I specified in the index file two groups: 10 ligands and
Glycine residue. So I have calculated hbonds (second column) and
collisions (third column) and then I made a sum of all frames
during 100 ns simualtion time (one frame every 50 ps) obtaining
1872 hbonds and 703 collisions between Glycine and 10 ligands. I
did it with every residue to assess binding affinity of
different amino acids.


I forgot to mention in the previous message that there is no value
in summing the hydrogen bonds over time.  Some of those H-bonds may
be distinct, and others may be the same H-bond that has broken and
subsequently re-formed.  I doubt anyone would find real value in
saying that 10 ligands formed 1872 H-bonds with glycine over a
trajectory.

-Justin

Obviosuly, but it can provide you some information about binding 
affinity - some ligands remains close to some residues longer than the 
others so by sum of this values you can assess residues with higher 
binding affinity.
 


The average number of hydrogen bonds over time will tell you the same thing, 
with much greater precision.  There are a maximum number of H-bonds that glycine 
can participate in, since it only has backbone groups to contribute, so if you 
find that, on average, there are 2.5 out of a possible 3 H-bonding sites 
occupied, th

Re: [gmx-users] pdb2gmx of nucleic acids with ffamber03 force field

[Justin A. Lemkul]

MARIA ICIAR FRADES ALZUETA wrote:

Dear all,

I am trying to pdb2gmx a a pdb file gcaa.pdb having nucleic acids using 
amber force field 03:

pdb2gmx -ff amber03 -f gcaa.pdb -o rna.pdb -p rna.top -water tip3p

I have two questions:
1.
The ffamber03.rtp file specifies that O2 from should be O to be 
recognized by the rtp file. When one substitutes this atom the program 
complains:

Fatal error:
Atom O in residue RC 4 was not found in rtp entry RC with 31 atoms
while sorting atoms.

Keeping the original pdb O2 works fine, althought O2 is not in the 
ffamber03.rtp  file. Is this fine?


The atom name (O2) and type (O) are distinct.  Names have to match so that 
pdb2gmx can assign the correct type.




2.
When doing: editconf -f gcaa.pdb -o this.pdb
The residues named H2'1 as mapped in the .rtp file they became 1H2'. The 
pdb2gmx works fine but I do not know how it works if the new 1H2' is not 
in the ffamber03.rtp file.




Hydrogen nomenclature can be annoying.  Everyone seems to have their own 
standard.  If the topology was produced without issue, then the parameters 
applied to the structure are fine.


-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] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:



On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:



On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Steven Neumann wrote:

   Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my
   ligands and every single residue using g_hbond. Looking
at the
   criteria adpoted by Gromacs I found impossible that number of
   hydrogen bonds were higher than number of collisions...
And what
   is interesting in one of my residue I obtained result like
   this... All Hbonds with Glycine - 1872, All Collisions 704.
Does anyone know how is it possible?
   


   I don't know how any of your numbers are possible (1872 H-bonds
   forming with a glycine?), or what you are defining as a collision
   and how you calculated it. Please provide the exact commands that
   you're using.  If you're equating a contact (e.g. from g_mindist)
   with a collision, then realize that the default criteria for a
   contact are very different than the geometric criteria for a
   hydrogen bond.

   -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

   >

   ====
   -- gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users

   >
   Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/Search

   > before
posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to gmx-users-requ...@gromacs.org

   >.

   Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists

   >


 My system is made of 10 ligands and one protein. I used command:
 g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
 Where I specified in the index file two groups: 10 ligands and
Glycine residue. So I have calculated hbonds (second column) and
collisions (third column) and then I made a sum of all frames
during 100 ns simualtion time (one frame every 50 ps) obtaining
1872 hbonds and 703 collisions between Glycine and 10 ligands. I
did it with every residue to assess binding affinity of
different amino acids.
Criteria for collision is distance <3.5 A, and fo hbond distance
<3.5 A and angle. So when calcualting hbond and collisions the
number of hbonds has has to be smaller while collision takes
into account hbonds as welll. I obtained results like this for
all other residues which seems to be correct. Am I right?  



No.  The second column is not inclusive of the first.  It counts the
number of atoms that are within hydrogen bonding distance, but do
not meet the criteria because of the angle between D-H-A.


-Justin

In this case number of collisions has to include number of hbonds.
If collision is counted as a distance <3.5 and hbond distance <3.5
plus angle D-H-A means that collisions covers hbonds... Explain
please whether I am wrong.



The second column lists the number of atom pairs that satisfy the distance 
requirement but do not satisfy the angle r

[gmx-users] Free energy calculation question

[Fabian Casteblanco]

Hello Justin,

I'm calculating the free energy of a drug in an alcohol solvent.  I
have a question referring to your free energy tutorial.  You mentioned
that decoupling of electrostatic interactions is linear and decoupling
of vdW can vary.  Is this true for your case of methanol in water or
for all cases?  When I ran my system of drug in ethanol solvent, I got
a non linear dG for both electrostatic and vdW.  Also, is there no
need to find dG of cav ( the free energy required to form the solute
cavity within the solvent) ?  I have attached some graphs.

Thanks for your help.  Your tutorial was extremely useful.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com


dG300_summary.agr
Description: application/grace


dG300_summary.agr
Description: application/grace
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Re: [gmx-users] g_hbond

[Steven Neumann]

Thank you for clarification Justin!!! The Manual is not as clear as you :P

Steven

On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>>
>>
>> On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Steven Neumann wrote:
>>
>>
>>
>>On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>> >> wrote:
>>
>>
>>
>>   Steven Neumann wrote:
>>
>>   Hi Gromacs Users,
>>I have calculated hydrogen bonds and collisions between my
>>   ligands and every single residue using g_hbond. Looking
>>at the
>>   criteria adpoted by Gromacs I found impossible that number
>> of
>>   hydrogen bonds were higher than number of collisions...
>>And what
>>   is interesting in one of my residue I obtained result like
>>   this... All Hbonds with Glycine - 1872, All Collisions 704.
>>Does anyone know how is it possible?
>>
>>   I don't know how any of your numbers are possible (1872 H-bonds
>>   forming with a glycine?), or what you are defining as a
>> collision
>>   and how you calculated it. Please provide the exact commands
>> that
>>   you're using.  If you're equating a contact (e.g. from
>> g_mindist)
>>   with a collision, then realize that the default criteria for a
>>   contact are very different than the geometric criteria for a
>>   hydrogen bond.
>>
>>   -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 
>>
>> >
>>
>>
>>   >
>> 
>> >>
>>
>>   ==**==
>>   -- gmx-users mailing listgmx-users@gromacs.org
>>
>>   **>
>>
>>
>>
>>   
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>
>> 
>> >
>>   
>> 
>>
>> 
>> >>
>>   Please search the archive at
>>   
>> http://www.gromacs.org/**Support/Mailing_Lists/Search
>>
>> 
>> >
>>   
>> 
>>
>> >>
>> before
>>posting!
>>   Please don't post (un)subscribe requests to the list. Use the
>> www
>>   interface or send it to gmx-users-requ...@gromacs.org
>>> >
>>   
>>> >>.
>>
>>   Can't post? Read
>>
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>> 
>> >
>>   
>> 
>>
>> 
>> >>
>>
>>
>> My system is made of 10 ligands and one protein. I used command:
>> g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
>> Where I specified in the index file two groups: 10 ligands and
>>Glycine residue. So I have calculated hbonds (sec

Re: [gmx-users] g_hbond

[Steven Neumann]

One question for Glycine it is easy to assess 3 possible hbonds which
can create as hydrogen is only one atom as a side chain.
How about other amino acids and their maximum hbonds they can create?

Steven

On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann wrote:

> Thank you for clarification Justin!!! The Manual is not as clear as you :P
>
> Steven
>
>   On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul wrote:
>
>>
>>
>> Steven Neumann wrote:
>>
>>>
>>>
>>> On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>Steven Neumann wrote:
>>>
>>>
>>>
>>>On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
>>>mailto:jalem...@vt.edu>
>>> >> wrote:
>>>
>>>
>>>
>>>   Steven Neumann wrote:
>>>
>>>   Hi Gromacs Users,
>>>I have calculated hydrogen bonds and collisions between my
>>>   ligands and every single residue using g_hbond. Looking
>>>at the
>>>   criteria adpoted by Gromacs I found impossible that number
>>> of
>>>   hydrogen bonds were higher than number of collisions...
>>>And what
>>>   is interesting in one of my residue I obtained result like
>>>   this... All Hbonds with Glycine - 1872, All Collisions 704.
>>>Does anyone know how is it possible?
>>>
>>>   I don't know how any of your numbers are possible (1872 H-bonds
>>>   forming with a glycine?), or what you are defining as a
>>> collision
>>>   and how you calculated it. Please provide the exact commands
>>> that
>>>   you're using.  If you're equating a contact (e.g. from
>>> g_mindist)
>>>   with a collision, then realize that the default criteria for a
>>>   contact are very different than the geometric criteria for a
>>>   hydrogen bond.
>>>
>>>   -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 
>>>
>>> >
>>>
>>>
>>>   >>
>>> 
>>> >>
>>>
>>>   ==**==
>>>   -- gmx-users mailing listgmx-users@gromacs.org
>>>
>>>   **>
>>>
>>>
>>>
>>>   
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>>
>>> 
>>> >
>>>   
>>> 
>>>
>>> 
>>> >>
>>>   Please search the archive at
>>>   
>>> http://www.gromacs.org/**Support/Mailing_Lists/Search
>>>
>>> 
>>> >
>>>   
>>> 
>>>
>>> >>
>>> before
>>>posting!
>>>   Please don't post (un)subscribe requests to the list. Use the
>>> www
>>>   interface or send it to gmx-users-requ...@gromacs.org
>>>
>>> >> >
>>>   
>>>
>>> >> >>.
>>>
>>>   Can't post? Read
>>>
>>> http://www.gromacs.org/**Support/Mailing_Lists
>>>
>>> 
>>> >
>>>   
>>> 
>>

Re: [gmx-users] g_hbond

[Justin A. Lemkul]

Steven Neumann wrote:
One question for Glycine it is easy to assess 3 possible hbonds 
which can create as hydrogen is only one atom as a side chain.

How about other amino acids and their maximum hbonds they can create?
 


Any OH or NH group is a donor, any lone pair is an acceptor (though obviously 
not modeled explicitly in MD).  The ability of MD force fields to agree with 
reality in this respect is debatable, but should come close.


-Justin


Steven

On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann > wrote:


Thank you for clarification Justin!!! The Manual is not as clear as
you :P
 
Steven


On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Steven Neumann wrote:



On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Steven Neumann wrote:



   On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

  | (540)

   231-9080 
  

  http://www.bevanlab.biochem
.
 
 vt.edu/Pages/Personal/__justin


   >

  vt.edu/Pages/Personal/justin

 
 >>

  ==__==
  -- gmx-users mailing list  
 gmx-users@gromacs.org 

   >
   >__>


 
http://lists.gromacs.org/__mailman/listinfo/gmx-users


 
 >
 

 
 

Re: [gmx-users] Free energy calculation question

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello Justin,

I'm calculating the free energy of a drug in an alcohol solvent.  I
have a question referring to your free energy tutorial.  You mentioned
that decoupling of electrostatic interactions is linear and decoupling
of vdW can vary.  Is this true for your case of methanol in water or
for all cases?  When I ran my system of drug in ethanol solvent, I got


I've never seen a case where (de)coupling of Coulombic interactions wasn't 
linear.  Since, for electrostatics, V is linearly dependent on lambda, I would 
expect this to generally be the case.  I don't know if nonlinearity is possible; 
maybe someone else can comment.  But generally, people use very few lambda 
values when (de)coupling charges from the system and linearity is generally 
achieved, with some minor variation towards the extreme values of lambda (close 
to 0 and 1).



a non linear dG for both electrostatic and vdW.  Also, is there no
need to find dG of cav ( the free energy required to form the solute
cavity within the solvent) ?  I have attached some graphs.



There is no explicit cavity term, but that's what happens when you turn on LJ 
interactions - the solute appears gradually within the solvent.


-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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[gmx-users] Re: Free energy calculation question

[Fabian Casteblanco]

Hello Justin,

I'm looking at the dG vs Lambda plot that is an output from G_bar but
on the Shirts et al paper that you included, the part where it talks
about linearity, it is referring to dH/dLambda for electrostatic
decoupling.  So if I take the line formed by dGtotal vs Lambda from
g_bar output and take the derivative excluding the beginning and end
parts (lambda approaches 0 and 1) then it does seem to take more of a
somewhat linear shape.  If you can see attached, I think perhaps thats
how I was misreading it?  I hope that can be the reason, since I've
done it with 4 different cases (2 different amount of solvent
molecules and using MD and SD integrator) and they all seem to be
giving similar results.

Thanks for your help.
-Fabian

On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco
 wrote:
> Hello Justin,
>
> I'm calculating the free energy of a drug in an alcohol solvent.  I
> have a question referring to your free energy tutorial.  You mentioned
> that decoupling of electrostatic interactions is linear and decoupling
> of vdW can vary.  Is this true for your case of methanol in water or
> for all cases?  When I ran my system of drug in ethanol solvent, I got
> a non linear dG for both electrostatic and vdW.  Also, is there no
> need to find dG of cav ( the free energy required to form the solute
> cavity within the solvent) ?  I have attached some graphs.
>
> Thanks for your help.  Your tutorial was extremely useful.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering PhD Student
> C: +908 917 0723
> E:  fabian.castebla...@gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
--
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Re: [gmx-users] Re: Free energy calculation question

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello Justin,

I'm looking at the dG vs Lambda plot that is an output from G_bar but
on the Shirts et al paper that you included, the part where it talks
about linearity, it is referring to dH/dLambda for electrostatic
decoupling.  So if I take the line formed by dGtotal vs Lambda from
g_bar output and take the derivative excluding the beginning and end
parts (lambda approaches 0 and 1) then it does seem to take more of a
somewhat linear shape.  If you can see attached, I think perhaps thats


You haven't attached anything.


how I was misreading it?  I hope that can be the reason, since I've
done it with 4 different cases (2 different amount of solvent
molecules and using MD and SD integrator) and they all seem to be
giving similar results.



That could be it.  The BAR output and the plots from TI are different.  Also be 
sure that you're not using soft-core for the Coulombic (de)coupling, as was 
suggested previously.


-Justin


Thanks for your help.
-Fabian

On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco
 wrote:

Hello Justin,

I'm calculating the free energy of a drug in an alcohol solvent.  I
have a question referring to your free energy tutorial.  You mentioned
that decoupling of electrostatic interactions is linear and decoupling
of vdW can vary.  Is this true for your case of methanol in water or
for all cases?  When I ran my system of drug in ethanol solvent, I got
a non linear dG for both electrostatic and vdW.  Also, is there no
need to find dG of cav ( the free energy required to form the solute
cavity within the solvent) ?  I have attached some graphs.

Thanks for your help.  Your tutorial was extremely useful.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com







--


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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[gmx-users] Re: Free energy calculation question

[Fabian Casteblanco]

Hello Justin,

You mean that only for vdW decoupling, you would need to use soft-core
potentials?  I had soft -core potentials on for decoupling the
electrostatic interactions (see below).   What would I use in its
place?  Thanks again for your help!


;Production MD
;
include =-I/mphase/users2/fabian/CGenff
title   =CGenFF Lov/Eth Solution MD run

;PARAMETERS - describing what to do, when to stop and what to save
;

;Run parameters
integrator  =sd ;leap-frog integrator
ld_seed =-1
nsteps  =50 ;2*50=1000ps, 1 ns
dt  =0.002  ;2 fs
nstcomm = 100   ;*** - frequency for center of mass
motion removal

;Output control
nstxout =1000   ;save coordinates every 2ps
nstvout =1000   ;save velocities every 2 ps
nstenergy   =1000   ;save energies every 2 ps
nstlog  =1000   ;update log file every 2 ps
nstxtcout   =1000   ;xtc compressed trajectory output every 
2 ps
xtc-precision   =1000   ;*** - precision to write to xtc 
trajectory

;Bond Parameters
continuation=yes;Restarting after NPT
constraint_algorithm=lincs  ;holonomic constraints
constraints =all-bonds  ;all bonds (even heavy atom-H bonds) 
constr;ained
lincs_iter  =1  ;accuracy of LINCS
lincs_order =12 ;also related to accuracy

;Neighborhood searching
ns_type =grid   ;search neighboring grid cells
nstlist =5  ;#steps.  5*0.002 ps = 5* 2 fs = 10 fs 
- Frequency to
update the neighbor list (and the long-range forces, when   
;using
twin-range cut-off’s). When this is 0, the neighbor list is made only
once.
rlist   =1.1;short-range neighborlist cutoff (in nm)
rcoulomb=1.1;short-range electrostatic cutoff (in 
nm)
pbc =xyz; 3-D PBC

;Electrostatics 
coulombtype =PME;Particle Mesh Ewald for long-range 
electrostat;ics
pme_order   =4  ;cubic interpolation
fourierspacing  =0.16   ;grid spacing for FFT

; van der Waals
vdwtype =Shift  ;Van der Waals for CHARMM
rvdw_switch =0.8
rvdw=1.0;Short-range Van der Waals cut-off

;Dispersion correction
DispCorr=EnerPres   ;account for cut-off vdW scheme

;Temperature coupling is on
tcoupl  =V-rescale  ;modified Berendsen thermostat
tc-grps =SYSTEM ;two coupling groups - more accurate
tau_t   =0.1;time constant, in ps
ref_t   =298;reference temperature, on for each 
group, in K

;Pressure coupling is on
pcoupl=Parrinello-Rahman;Pressure coupling on in NPT
pcoupltype  =isotropic ;uniform scaling of box 
vect;ors
tau_p   =2.0   ;time constant, in ps
ref_p   =1.0   ;reference pressure, in bar
compressibility =4.5e-5;isothermal compr of H2O, 
ba;r^(-1)

; Free energy control stuff
free_energy = yes   ;*** - Indicates we are doing a free
energy calculation, and that interpolation between the A and B states
of the  ;chosen molecule (defined 
below) will occur.
init_lambda = 0.0   ;*** - Value of λ
delta_lambda= 0 ;*** - The value of λ can be incremented
by some amount per timestep (i.e., δλ/δt) in a technique called "slow
;growth." This method can have 
significant errors associated
with it, and thus we will make no time-dependent
;changes to our
λ values.
foreign_lambda  = 0.05  ;*** - Additional values of λ for
which ΔH will be written to dhdl.xvg (with frequency nstdhdl). The
;configurations generated in 
the trajectory at λ = init_lambda
will have ΔH calculated for these same  
;configurations at all
values of λ = foreign_lambda.
sc-alpha= 0.5   ;*** - the soft-core parameter, a value
of 0 results in linear interpolation of the LJ and Coulomb
;interactions
sc-power= 1.0   ;*** - the power for lambda in the
soft-core function, only the values 1 and 2 are supported
sc-sigma

Re: [gmx-users] Re: Free energy calculation question

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello Justin,

You mean that only for vdW decoupling, you would need to use soft-core
potentials?  I had soft -core potentials on for decoupling the
electrostatic interactions (see below).   What would I use in its
place?  Thanks again for your help!



You only need soft-core for LJ transformations.  Set sc_alpha to 0 (as you have 
noted in the comment) for normal (linear) interpolation.


-Justin



;Production MD
;
include =-I/mphase/users2/fabian/CGenff
title   =CGenFF Lov/Eth Solution MD run

;PARAMETERS - describing what to do, when to stop and what to save
;

;Run parameters
integrator  =sd ;leap-frog integrator
ld_seed =-1
nsteps  =50 ;2*50=1000ps, 1 ns
dt  =0.002  ;2 fs
nstcomm = 100   ;*** - frequency for center of mass
motion removal

;Output control
nstxout =1000   ;save coordinates every 2ps
nstvout =1000   ;save velocities every 2 ps
nstenergy   =1000   ;save energies every 2 ps
nstlog  =1000   ;update log file every 2 ps
nstxtcout   =1000   ;xtc compressed trajectory output every 
2 ps
xtc-precision   =1000   ;*** - precision to write to xtc 
trajectory

;Bond Parameters
continuation=yes;Restarting after NPT
constraint_algorithm=lincs  ;holonomic constraints
constraints =all-bonds  ;all bonds (even heavy atom-H bonds) 
constr;ained
lincs_iter  =1  ;accuracy of LINCS
lincs_order =12 ;also related to accuracy

;Neighborhood searching
ns_type =grid   ;search neighboring grid cells
nstlist =5  ;#steps.  5*0.002 ps = 5* 2 fs = 10 fs 
- Frequency to
update the neighbor list (and the long-range forces, when   
;using
twin-range cut-off’s). When this is 0, the neighbor list is made only
once.
rlist   =1.1;short-range neighborlist cutoff (in nm)
rcoulomb=1.1;short-range electrostatic cutoff (in 
nm)
pbc =xyz; 3-D PBC

;Electrostatics 
coulombtype =PME;Particle Mesh Ewald for long-range 
electrostat;ics
pme_order   =4  ;cubic interpolation
fourierspacing  =0.16   ;grid spacing for FFT

; van der Waals
vdwtype =Shift  ;Van der Waals for CHARMM
rvdw_switch =0.8
rvdw=1.0;Short-range Van der Waals cut-off

;Dispersion correction
DispCorr=EnerPres   ;account for cut-off vdW scheme

;Temperature coupling is on
tcoupl  =V-rescale  ;modified Berendsen thermostat
tc-grps =SYSTEM ;two coupling groups - more accurate
tau_t   =0.1;time constant, in ps
ref_t   =298;reference temperature, on for each 
group, in K

;Pressure coupling is on
pcoupl=Parrinello-Rahman;Pressure coupling on in NPT
pcoupltype  =isotropic ;uniform scaling of box 
vect;ors
tau_p   =2.0   ;time constant, in ps
ref_p   =1.0   ;reference pressure, in bar
compressibility =4.5e-5;isothermal compr of H2O, 
ba;r^(-1)

; Free energy control stuff
free_energy = yes   ;*** - Indicates we are doing a free
energy calculation, and that interpolation between the A and B states
of the  ;chosen molecule (defined 
below) will occur.
init_lambda = 0.0   ;*** - Value of λ
delta_lambda= 0 ;*** - The value of λ can be incremented
by some amount per timestep (i.e., δλ/δt) in a technique called "slow
;growth." This method can have 
significant errors associated
with it, and thus we will make no time-dependent
;changes to our
λ values.
foreign_lambda  = 0.05  ;*** - Additional values of λ for
which ΔH will be written to dhdl.xvg (with frequency nstdhdl). The
;configurations generated in 
the trajectory at λ = init_lambda
will have ΔH calculated for these same  
;configurations at all
values of λ = foreign_lambda.
sc-alpha= 0.5   ;*** - the soft-core parameter, a value
of 0 results in linear interpolation of the LJ and Coulomb
 

[gmx-users] Re: Free energy calculation question

[Fabian Casteblanco]

Thanks Justin!

On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco
 wrote:
> Hello Justin,
>
> I'm calculating the free energy of a drug in an alcohol solvent.  I
> have a question referring to your free energy tutorial.  You mentioned
> that decoupling of electrostatic interactions is linear and decoupling
> of vdW can vary.  Is this true for your case of methanol in water or
> for all cases?  When I ran my system of drug in ethanol solvent, I got
> a non linear dG for both electrostatic and vdW.  Also, is there no
> need to find dG of cav ( the free energy required to form the solute
> cavity within the solvent) ?  I have attached some graphs.
>
> Thanks for your help.  Your tutorial was extremely useful.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering PhD Student
> C: +908 917 0723
> E:  fabian.castebla...@gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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[gmx-users] doubt in deuterium order parameter

[Parthasarathi, Ramya]

Hi,

I am trying to write a code for Deuterium order parameter of DOPC lipid. I went 
through the code in gmx_order.c, I did the following,


1.   I took the carbons in the chain, and found its neighbors.

2.   Took the bilayer normal and found the angle between the bilayer normal 
and the -CH molecular axis.

3.   Took care of the periodic boundary conditions since I use NPT ensemble.

But the code in gmx_order.c in GROMACS tries to do a lot of things other than 
this, as I don't know C or C++ language that it is using, I don't know what 
else I am supposed to include.

Can someone please help me?

Ramya
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[gmx-users] order parameter

[Parthasarathi, Ramya]

Hi,

I am trying to write a code for Deuterium order parameter of DOPC lipid. I went 
through the code in gmx_order.c, I did the following,

1.   I took the carbons in the chain, and found its neighbors.
2.   Took the bilayer normal and found the angle between the bilayer normal 
and the –CH molecular axis.
3.   Took care of the periodic boundary conditions since I use NPT ensemble.

But the code in gmx_order.c in GROMACS tries to do a lot of things other than 
this, as I don’t know C or C++ language that it is using, I don’t know what 
else I am supposed to include.

Can someone please help me?

Ramya
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[gmx-users] which charge is used in gromacs program

[GZ Zhang]

Hi, ALL

  I have a question about the charge defined in the topology file.
  It seems to me that the charge for each atom apprears twice in
different sections of the topology files.
--
  One is
[ atomtypes ]
;name mass  charge   ptype   c6c12

  The other is
[ atoms ]
; idat type res nr  residu name at name cg nr   charge
--
   And the charge number in [ atomtypes ] are always 0.0.
   Which one is actually read by gromacs program ?

   Thanks,

Guozhen Zhang
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Re: [gmx-users] which charge is used in gromacs program

[Justin A. Lemkul]

GZ Zhang wrote:

Hi, ALL

  I have a question about the charge defined in the topology file.
  It seems to me that the charge for each atom apprears twice in 
different sections of the topology files.

--
  One is 
[ atomtypes ]

;name mass  charge   ptype   c6c12

  The other is
[ atoms ]
; idat type res nr  residu name at name cg nr   charge
--
   And the charge number in [ atomtypes ] are always 0.0.
   Which one is actually read by gromacs program ?



The charge listed in [atoms].  You can always verify your .tpr file with 
gmxdump.

-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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[gmx-users] Re: which charge is used in gromacs program

[Dr. Vitaly V. Chaban]

>
> Hi, ALL
>
>      I have a question about the charge defined in the topology file.
>      It seems to me that the charge for each atom apprears twice in
> different sections of the topology files.
> --
>      One is
> [ atomtypes ]
> ;name     mass      charge   ptype   c6            c12
>
>      The other is
> [ atoms ]
> ; id    at type res nr  residu name at name cg nr   charge
> --
>       And the charge number in [ atomtypes ] are always 0.0.
>       Which one is actually read by gromacs program ?


That one which is mentioned the last



-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

[Itamar Kass]

Hi Chris,

Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 
again, now starting from a 5 ns simulations run using 4.0.7, and again the 
simulations had stopped after 1000 LINCS error (I can extend the simulations 
using 4.0.7). 

I know that gromacs stopped after 1000 LINCS, but this is usually a sign that 
something bad is going on in the system.

Cheers,
Itamar

On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote:

> OK, here's my last few ideas:
> 
> 1. Please try to repeat this with gen_vel set to the same value as your 
> temperature coupling
> 
> 2. Can you reproduce this in serial?
> 
> 3. Can you reproduce this with the sd integrator?
> 
> 4. Can you reproduce this with a simpler system? protein in vacuum or just 
> water or remove the ions, etc?
> 
> 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 
> 4.5.4. Do you get the same lincs warnings?
> 
> 6. Also, note that you are getting warnings and the run does not actually 
> crash but just stops after too many warnings. So what are atoms 981 and 982? 
> Does their motion look different in an important ways between the 4.0.7 and 
> 4.5.4 trajectories?
> 
> Chris.
> 
> -- original message --
> 
> Hi Chris,
> 
> thanks for the advice, I have to say I tried this as well without any success.
> 
> Itamar
> 
> On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:
> 
>> run an EM with flexible water. I often find that this is the only way to get 
>> a stable system. 500 steps of steep with define=-DFLEXIBLE (or different 
>> depending on your water model I think) should be enough.
>> 
>> Chris.
>> 
>> Hi Chris and Justin,
>> 
>> On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
>> 
> 
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-
"In theory, there is no difference between theory and practice. But, in 
practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu


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Re: [gmx-users] Re: which charge is used in gromacs program

[Justin A. Lemkul]

Dr. Vitaly V. Chaban wrote:

Hi, ALL

 I have a question about the charge defined in the topology file.
 It seems to me that the charge for each atom apprears twice in
different sections of the topology files.
--
 One is
[ atomtypes ]
;name mass  charge   ptype   c6c12

 The other is
[ atoms ]
; idat type res nr  residu name at name cg nr   charge
--
  And the charge number in [ atomtypes ] are always 0.0.
  Which one is actually read by gromacs program ?



That one which is mentioned the last



That is true in the case where grompp finds multiply defined types for bonded 
interactions and atom types; the charges in ffnonbonded.itp are never used by 
any program.  The reason for their existence is not clear, but perhaps they were 
used by older versions or were intended for some streamlined force field 
organization that never came to fruition.


-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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[gmx-users] Invitation to connect on LinkedIn

[Hideya Nakamura via LinkedIn]

LinkedIn





Hideya Nakamura requested to add you as a connection on LinkedIn:
  
--

Chinmay,

I'd like to add you to my professional network on LinkedIn.

- Hideya

Accept invitation from Hideya Nakamura
http://www.linkedin.com/e/-85v1n9-gs0zpsj1-6n/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I3076163352_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnP8RcPcScjoTc3d9bSJeuAkMpBp4bPsPcjcOejwQc3gLrCBxbOYWrSlI/EML_comm_afe/?hs=false&tok=1RiHO-b01mokU1

View profile of Hideya Nakamura
http://www.linkedin.com/e/-85v1n9-gs0zpsj1-6n/rsn/49917431/iCi0/?hs=false&tok=3HlH7Lty5mokU1
--

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Re: [gmx-users] Re: which charge is used in gromacs program

[Dr. Vitaly V. Chaban]

On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul  wrote:
>
>
> Dr. Vitaly V. Chaban wrote:
>>>
>>> Hi, ALL
>>>
>>>     I have a question about the charge defined in the topology file.
>>>     It seems to me that the charge for each atom apprears twice in
>>> different sections of the topology files.
>>>
>>> --
>>>     One is
>>> [ atomtypes ]
>>> ;name     mass      charge   ptype   c6            c12
>>>
>>>     The other is
>>> [ atoms ]
>>> ; id    at type res nr  residu name at name cg nr   charge
>>>
>>> --
>>>      And the charge number in [ atomtypes ] are always 0.0.
>>>      Which one is actually read by gromacs program ?
>>
>>
>> That one which is mentioned the last
>>
>
> That is true in the case where grompp finds multiply defined types for
> bonded interactions and atom types; the charges in ffnonbonded.itp are never
> used by any program.  The reason for their existence is not clear, but
> perhaps they were used by older versions or were intended for some
> streamlined force field organization that never came to fruition.
>


I believe, this column is intended for aminoacids for which there
should be a consistent set of parameters including charges. This is
what we have in AMBER.




-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] Re: which charge is used in gromacs program

[Mark Abraham]

On 1/09/2011 10:34 AM, Dr. Vitaly V. Chaban wrote:

On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul  wrote:


Dr. Vitaly V. Chaban wrote:

Hi, ALL

 I have a question about the charge defined in the topology file.
 It seems to me that the charge for each atom apprears twice in
different sections of the topology files.

--
 One is
[ atomtypes ]
;name mass  charge   ptype   c6c12

 The other is
[ atoms ]
; idat type res nr  residu name at name cg nr   charge

--
  And the charge number in [ atomtypes ] are always 0.0.
  Which one is actually read by gromacs program ?


That one which is mentioned the last


That is true in the case where grompp finds multiply defined types for
bonded interactions and atom types; the charges in ffnonbonded.itp are never
used by any program.  The reason for their existence is not clear, but
perhaps they were used by older versions or were intended for some
streamlined force field organization that never came to fruition.



I believe, this column is intended for aminoacids for which there
should be a consistent set of parameters including charges. This is
what we have in AMBER.


However that only works if the charge is the same for that atom type in 
each possible residue. That's not a very effective constraint.


Mark
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Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

[Mark Abraham]

On 1/09/2011 10:20 AM, Itamar Kass wrote:

Hi Chris,

Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 
again, now starting from a 5 ns simulations run using 4.0.7, and again the 
simulations had stopped after 1000 LINCS error (I can extend the simulations 
using 4.0.7).

I know that gromacs stopped after 1000 LINCS, but this is usually a sign that 
something bad is going on in the system.


OK. Chris suggested a number of other strategies that will help 
determine which aspect of 4.5.4 is behaving differently. How did those 
strategies work out?


Mark



Cheers,
Itamar

On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote:


OK, here's my last few ideas:

1. Please try to repeat this with gen_vel set to the same value as your 
temperature coupling

2. Can you reproduce this in serial?

3. Can you reproduce this with the sd integrator?

4. Can you reproduce this with a simpler system? protein in vacuum or just 
water or remove the ions, etc?

5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 
4.5.4. Do you get the same lincs warnings?

6. Also, note that you are getting warnings and the run does not actually crash 
but just stops after too many warnings. So what are atoms 981 and 982? Does 
their motion look different in an important ways between the 4.0.7 and 4.5.4 
trajectories?

Chris.

-- original message --

Hi Chris,

thanks for the advice, I have to say I tried this as well without any success.

Itamar

On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:


run an EM with flexible water. I often find that this is the only way to get a 
stable system. 500 steps of steep with define=-DFLEXIBLE (or different 
depending on your water model I think) should be enough.

Chris.

Hi Chris and Justin,

On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:



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-
"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu




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[gmx-users] order parameter

[chris . neale]

Dear Ramya:

Are you simulating all-atom lipids (with explicit hydrogen atoms on  
the acyl chain)? If not, then you missed a step in your description of  
what you have done (g_order, for example, ignores explicit hydrogen  
atoms so that it can act on united atom lipids).


Not sure why PBC would be your step #3, after your step #2 was to find  
the angle. I suggest that you simply run trjconv -pbc mol on your  
trajectory file before you process it and then you no longer need to  
worry about PBC in your custom analysis tool.


Once you have the angle, you must average it correctly. The equation  
is available in most papers that describe order parameters and is  
listed as a comment at the top of the gmx_order.c source file (in  
version 4.0.7 at least).


If you want to get more help on your procedure after you have worked  
on this for a while, I suggest laying out your procedure very  
specifically. Your previous post, for example, was pretty loose with  
terminology when you described your method and there is quite a bit  
that one must assume.


Chris.

-- original message --

Hi,

I am trying to write a code for Deuterium order parameter of DOPC  
lipid. I went through the code in gmx_order.c, I did the following,


1.   I took the carbons in the chain, and found its neighbors.
2.   Took the bilayer normal and found the angle between the  
bilayer normal and the ?CH molecular axis.
3.   Took care of the periodic boundary conditions since I use NPT  
ensemble.


But the code in gmx_order.c in GROMACS tries to do a lot of things  
other than this, as I don?t know C or C++ language that it is using, I  
don?t know what else I am supposed to include.


Can someone please help me?

Ramya


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Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

[Itamar Kass]

Hi Mark,

I didn't had the time to do the SD yet, but serial run end with the same 
results. I didn't try water only system, as this is of no interest to me, but I 
will simplify the system later on.

Cheers,
Itamar

On 01/09/2011, at 10:51 AM, Mark Abraham wrote:

> On 1/09/2011 10:20 AM, Itamar Kass wrote:
>> Hi Chris,
>> 
>> Thanks for the email, I am sorry it took me some time to replay. I tried 
>> 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again 
>> the simulations had stopped after 1000 LINCS error (I can extend the 
>> simulations using 4.0.7).
>> 
>> I know that gromacs stopped after 1000 LINCS, but this is usually a sign 
>> that something bad is going on in the system.
> 
> OK. Chris suggested a number of other strategies that will help determine 
> which aspect of 4.5.4 is behaving differently. How did those strategies work 
> out?
> 
> Mark
> 
>> 
>> Cheers,
>> Itamar
>> 
>> On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote:
>> 
>>> OK, here's my last few ideas:
>>> 
>>> 1. Please try to repeat this with gen_vel set to the same value as your 
>>> temperature coupling
>>> 
>>> 2. Can you reproduce this in serial?
>>> 
>>> 3. Can you reproduce this with the sd integrator?
>>> 
>>> 4. Can you reproduce this with a simpler system? protein in vacuum or just 
>>> water or remove the ions, etc?
>>> 
>>> 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 
>>> 4.5.4. Do you get the same lincs warnings?
>>> 
>>> 6. Also, note that you are getting warnings and the run does not actually 
>>> crash but just stops after too many warnings. So what are atoms 981 and 
>>> 982? Does their motion look different in an important ways between the 
>>> 4.0.7 and 4.5.4 trajectories?
>>> 
>>> Chris.
>>> 
>>> -- original message --
>>> 
>>> Hi Chris,
>>> 
>>> thanks for the advice, I have to say I tried this as well without any 
>>> success.
>>> 
>>> Itamar
>>> 
>>> On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:
>>> 
 run an EM with flexible water. I often find that this is the only way to 
 get a stable system. 500 steps of steep with define=-DFLEXIBLE (or 
 different depending on your water model I think) should be enough.
 
 Chris.
 
 Hi Chris and Justin,
 
 On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
 
>>> 
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> -
>> "In theory, there is no difference between theory and practice. But, in 
>> practice, there is." - Jan L.A. van de Snepscheut
>> 
>> ===
>> | Itamar Kass, Ph.D.
>> | Postdoctoral Research Fellow
>> |
>> | Department of Biochemistry and Molecular Biology
>> | Building 77 Clayton Campus
>> | Wellington Road
>> | Monash University,
>> | Victoria 3800
>> | Australia
>> |
>> | Tel: +61 3 9902 9376
>> | Fax: +61 3 9902 9500
>> | E-mail: itamar.k...@monash.edu
>> 
>> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-
"In theory, there is no difference between theory and practice. But, in 
practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu


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Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

[Justin A. Lemkul]

Itamar Kass wrote:

Hi Mark,

I didn't had the time to do the SD yet, but serial run end with the same 
results. I didn't try water only system, as this is of no interest to me, but I 
will simplify the system later on.



Being of interest to you and being a useful diagnostic may be different.  It's 
important to rule out different variables to arrive at a solution, which I 
suspect is of interest to you.  You also haven't addressed points #1 and #6 in 
Chris' message.


-Justin


Cheers,
Itamar

On 01/09/2011, at 10:51 AM, Mark Abraham wrote:


On 1/09/2011 10:20 AM, Itamar Kass wrote:

Hi Chris,

Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 
again, now starting from a 5 ns simulations run using 4.0.7, and again the 
simulations had stopped after 1000 LINCS error (I can extend the simulations 
using 4.0.7).

I know that gromacs stopped after 1000 LINCS, but this is usually a sign that 
something bad is going on in the system.

OK. Chris suggested a number of other strategies that will help determine which 
aspect of 4.5.4 is behaving differently. How did those strategies work out?

Mark


Cheers,
Itamar

On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote:


OK, here's my last few ideas:

1. Please try to repeat this with gen_vel set to the same value as your 
temperature coupling

2. Can you reproduce this in serial?

3. Can you reproduce this with the sd integrator?

4. Can you reproduce this with a simpler system? protein in vacuum or just 
water or remove the ions, etc?

5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 
4.5.4. Do you get the same lincs warnings?

6. Also, note that you are getting warnings and the run does not actually crash 
but just stops after too many warnings. So what are atoms 981 and 982? Does 
their motion look different in an important ways between the 4.0.7 and 4.5.4 
trajectories?

Chris.

-- original message --

Hi Chris,

thanks for the advice, I have to say I tried this as well without any success.

Itamar

On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:


run an EM with flexible water. I often find that this is the only way to get a 
stable system. 500 steps of steep with define=-DFLEXIBLE (or different 
depending on your water model I think) should be enough.

Chris.

Hi Chris and Justin,

On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:


--
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-
"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu



--
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Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-
"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu




--


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] GROMACS 4.5.4 keep crashing all the time

[Itamar Kass]

Hi Justin,

I did repeat it using gen_val and running temperature the same, with no effect, 
it is still crash. I didn't replied point #6 because the atoms which triggers 
the LINCS are different between each try. Sometimes it is the peptide N and H, 
like in the case of 981 and 982, and sometimes others. In addition, there is no 
visible difference in dynamics between 4.0.7 and 4.5.4 I can find.

Itamar 


On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote:

> 
> 
> Itamar Kass wrote:
>> Hi Mark,
>> I didn't had the time to do the SD yet, but serial run end with the same 
>> results. I didn't try water only system, as this is of no interest to me, 
>> but I will simplify the system later on.
> 
> Being of interest to you and being a useful diagnostic may be different.  
> It's important to rule out different variables to arrive at a solution, which 
> I suspect is of interest to you.  You also haven't addressed points #1 and #6 
> in Chris' message.
> 
> -Justin
> 
>> Cheers,
>> Itamar
>> On 01/09/2011, at 10:51 AM, Mark Abraham wrote:
>>> On 1/09/2011 10:20 AM, Itamar Kass wrote:
 Hi Chris,
 
 Thanks for the email, I am sorry it took me some time to replay. I tried 
 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and 
 again the simulations had stopped after 1000 LINCS error (I can extend the 
 simulations using 4.0.7).
 
 I know that gromacs stopped after 1000 LINCS, but this is usually a sign 
 that something bad is going on in the system.
>>> OK. Chris suggested a number of other strategies that will help determine 
>>> which aspect of 4.5.4 is behaving differently. How did those strategies 
>>> work out?
>>> 
>>> Mark
>>> 
 Cheers,
 Itamar
 
 On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote:
 
> OK, here's my last few ideas:
> 
> 1. Please try to repeat this with gen_vel set to the same value as your 
> temperature coupling
> 
> 2. Can you reproduce this in serial?
> 
> 3. Can you reproduce this with the sd integrator?
> 
> 4. Can you reproduce this with a simpler system? protein in vacuum or 
> just water or remove the ions, etc?
> 
> 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it 
> under 4.5.4. Do you get the same lincs warnings?
> 
> 6. Also, note that you are getting warnings and the run does not actually 
> crash but just stops after too many warnings. So what are atoms 981 and 
> 982? Does their motion look different in an important ways between the 
> 4.0.7 and 4.5.4 trajectories?
> 
> Chris.
> 
> -- original message --
> 
> Hi Chris,
> 
> thanks for the advice, I have to say I tried this as well without any 
> success.
> 
> Itamar
> 
> On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:
> 
>> run an EM with flexible water. I often find that this is the only way to 
>> get a stable system. 500 steps of steep with define=-DFLEXIBLE (or 
>> different depending on your water model I think) should be enough.
>> 
>> Chris.
>> 
>> Hi Chris and Justin,
>> 
>> On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
>> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 -
 "In theory, there is no difference between theory and practice. But, in 
 practice, there is." - Jan L.A. van de Snepscheut
 
 ===
 | Itamar Kass, Ph.D.
 | Postdoctoral Research Fellow
 |
 | Department of Biochemistry and Molecular Biology
 | Building 77 Clayton Campus
 | Wellington Road
 | Monash University,
 | Victoria 3800
 | Australia
 |
 | Tel: +61 3 9902 9376
 | Fax: +61 3 9902 9500
 | E-mail: itamar.k...@monash.edu
 
 
>>> -- 
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www interface 
>>> or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> -
>> "In theory, there is no difference between theory and practice. But, in 
>> practice, there is." - Jan L.A. van de Snepscheut
>> ===
>> | Itamar Kass, Ph.D.
>> | Postdoctoral Research Fellow
>> |
>> | Department of Biochemistry and 

[gmx-users] GROMACS 4.5.4 keep crashing all the time

[chris . neale]

Itamar:

We really are trying to help. I think that perhaps you don't grasp how  
difficult it is to help without being able to access the simulation  
directly. Therefore we have ideas and we ask you to do specific things  
that are going to move us toward a solution, either by finding answers  
or by ruling out possibilities.


It is actually useful information to know that "Sometimes it is the  
peptide N and H, like in the case of 981 and 982, and sometimes  
others" ... but when it seems like you don't want to provide the  
requested information my first inclination is to give up on trying to  
help.


At this point, there are a few unanswered old questions and I have  
some new questions.


1. Can you reproduce this with a water box?
2. Can you reproduce this with your protein in vacuum?
3. If neither 2 or 3, then can you step slowly from one of these  
systems toward your final system and identify the point at which the  
lincs warnings arise?

4. Do you get the warnings without Ca also, or just with Ca?
5. Can you reproduce this with the SD integrator? If you are really  
against trying this, then at least can you reproduce this with a  
single Berendsen temperature coupling group?
6. Can you reproduce this without using the reaction field? Either  
with PME or a simple cutoff?
7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4)  
where you start to see this warning?


Chris.

-- original message --

Hi Justin,

I did repeat it using gen_val and running temperature the same, with  
no effect, it is still crash. I didn't replied point #6 because the  
atoms which triggers the LINCS are different between each try.  
Sometimes it is the peptide N and H, like in the case of 981 and 982,  
and sometimes others. In addition, there is no visible difference in  
dynamics between 4.0.7 and 4.5.4 I can find.


Itamar


On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote:




Itamar Kass wrote:

Hi Mark,
I didn't had the time to do the SD yet, but serial run end with the  
same results. I didn't try water only system, as this is of no  
interest to me, but I will simplify the system later on.


Being of interest to you and being a useful diagnostic may be  
different.  It's important to rule out different variables to arrive  
at a solution, which I suspect is of interest to you.  You also  
haven't addressed points #1 and #6 in Chris' message.


-Justin


Cheers,
Itamar
On 01/09/2011, at 10:51 AM, Mark Abraham wrote:

On 1/09/2011 10:20 AM, Itamar Kass wrote:

Hi Chris,

Thanks for the email, I am sorry it took me some time to replay.  
I tried 4.5.4 again, now starting from a 5 ns simulations run  
using 4.0.7, and again the simulations had stopped after 1000  
LINCS error (I can extend the simulations using 4.0.7).


I know that gromacs stopped after 1000 LINCS, but this is usually  
a sign that something bad is going on in the system.
OK. Chris suggested a number of other strategies that will help  
determine which aspect of 4.5.4 is behaving differently. How did  
those strategies work out?


Mark


Cheers,
Itamar

On 18/08/2011, at 12:03 PM, chris.neale at utoronto.ca wrote:


OK, here's my last few ideas:

1. Please try to repeat this with gen_vel set to the same value  
as your temperature coupling


2. Can you reproduce this in serial?

3. Can you reproduce this with the sd integrator?

4. Can you reproduce this with a simpler system? protein in  
vacuum or just water or remove the ions, etc?


5. Take the output .gro from 4.0.7 that ran fine for X ns and  
run it under 4.5.4. Do you get the same lincs warnings?


6. Also, note that you are getting warnings and the run does not  
actually crash but just stops after too many warnings. So what  
are atoms 981 and 982? Does their motion look different in an  
important ways between the 4.0.7 and 4.5.4 trajectories?


Chris.

-- original message --

Hi Chris,

thanks for the advice, I have to say I tried this as well  
without any success.


Itamar

On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:

run an EM with flexible water. I often find that this is the  
only way to get a stable system. 500 steps of steep with  
define=-DFLEXIBLE (or different depending on your water model I  
think) should be enough.


Chris.

Hi Chris and Justin,

On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:


--
gmx-users mailing listgmx-users at gromacs.org
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-
"In theory, there is no difference between theory and practice.  
But, in practice, there is." - Jan L.A. van de Snepscheut


===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Bio

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

[Itamar Kass]

HI Chris,

I am sorry that from my mails it is seems like I am not appreciate the help, 
because I appreciate it much. It is just the fact that I am trying to give as 
much info as I can and to go over any idea in the mailing list without actually 
delay my other stuff. So again, I wish thanks for anyone who is helps here.

 
On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote:

> Itamar:
> 
> We really are trying to help. I think that perhaps you don't grasp how 
> difficult it is to help without being able to access the simulation directly. 
> Therefore we have ideas and we ask you to do specific things that are going 
> to move us toward a solution, either by finding answers or by ruling out 
> possibilities.
> 
> It is actually useful information to know that "Sometimes it is the peptide N 
> and H, like in the case of 981 and 982, and sometimes others" ... but when it 
> seems like you don't want to provide the requested information my first 
> inclination is to give up on trying to help.
> 
> At this point, there are a few unanswered old questions and I have some new 
> questions.
> 
> 1. Can you reproduce this with a water box?

The error is reproducible in a box of protein and water only.

> 2. Can you reproduce this with your protein in vacuum?

The error is reproduced in vacuum.

> 3. If neither 2 or 3, then can you step slowly from one of these systems 
> toward your final system and identify the point at which the lincs warnings 
> arise?
> 4. Do you get the warnings without Ca also, or just with Ca?

I am not sure what this mean. I get this warning mainly for N-H, but also for 
Ca-C, pairs of atoms 

> 5. Can you reproduce this with the SD integrator? If you are really against 
> trying this, then at least can you reproduce this with a single Berendsen 
> temperature coupling group?

When I use SD integrator, the simulations run fine.

> 6. Can you reproduce this without using the reaction field? Either with PME 
> or a simple cutoff?

Using PME the system is running just fine.

> 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where 
> you start to see this warning?

I can't tell, 'cause I jump from 4.0.7 to 4.5.4.

Thanks for the help,
Itamar

> 
> Chris.
> 
> -- original message --
> 
> Hi Justin,
> 
> I did repeat it using gen_val and running temperature the same, with no 
> effect, it is still crash. I didn't replied point #6 because the atoms which 
> triggers the LINCS are different between each try. Sometimes it is the 
> peptide N and H, like in the case of 981 and 982, and sometimes others. In 
> addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 
> I can find.
> 
> Itamar
> 
> 
> On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote:
> 
>> 
>> 
>> Itamar Kass wrote:
>>> Hi Mark,
>>> I didn't had the time to do the SD yet, but serial run end with the same 
>>> results. I didn't try water only system, as this is of no interest to me, 
>>> but I will simplify the system later on.
>> 
>> Being of interest to you and being a useful diagnostic may be different.  
>> It's important to rule out different variables to arrive at a solution, 
>> which I suspect is of interest to you.  You also haven't addressed points #1 
>> and #6 in Chris' message.
>> 
>> -Justin
>> 
>>> Cheers,
>>> Itamar
>>> On 01/09/2011, at 10:51 AM, Mark Abraham wrote:
 On 1/09/2011 10:20 AM, Itamar Kass wrote:
> Hi Chris,
> 
> Thanks for the email, I am sorry it took me some time to replay. I tried 
> 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and 
> again the simulations had stopped after 1000 LINCS error (I can extend 
> the simulations using 4.0.7).
> 
> I know that gromacs stopped after 1000 LINCS, but this is usually a sign 
> that something bad is going on in the system.
 OK. Chris suggested a number of other strategies that will help determine 
 which aspect of 4.5.4 is behaving differently. How did those strategies 
 work out?
 
 Mark
 
> Cheers,
> Itamar
> 
> On 18/08/2011, at 12:03 PM, chris.neale at utoronto.ca wrote:
> 
>> OK, here's my last few ideas:
>> 
>> 1. Please try to repeat this with gen_vel set to the same value as your 
>> temperature coupling
>> 
>> 2. Can you reproduce this in serial?
>> 
>> 3. Can you reproduce this with the sd integrator?
>> 
>> 4. Can you reproduce this with a simpler system? protein in vacuum or 
>> just water or remove the ions, etc?
>> 
>> 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it 
>> under 4.5.4. Do you get the same lincs warnings?
>> 
>> 6. Also, note that you are getting warnings and the run does not 
>> actually crash but just stops after too many warnings. So what are atoms 
>> 981 and 982? Does their motion look different in an important ways 
>> between the 4.0.7 and 4.5.4 trajectories?
>> 
>> Chris

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

[Tsjerk Wassenaar]

Hi Itamar,

I haven't really followed the discussion and I'm a bit too lazy to
look it all up now ;) But have you tried setting the nst parameters to
1  (except for output). Especially nstpcouple. Note that nstpcouple=1
requires nstlist=1 and nstcalcenergy=1. If that solves the problem,
you may need to extend your equilibration a bit, first relaxing NVT,
followed by NPT with nstpcouple=1, thereafter equilibrating using
productions conditions. It it solves it, maybe the option should be
renamed nstptrouble :p

Hope it helps,

Tsjerk

On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass  wrote:
> HI Chris,
>
> I am sorry that from my mails it is seems like I am not appreciate the help, 
> because I appreciate it much. It is just the fact that I am trying to give as 
> much info as I can and to go over any idea in the mailing list without 
> actually delay my other stuff. So again, I wish thanks for anyone who is 
> helps here.
>
>
> On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote:
>
>> Itamar:
>>
>> We really are trying to help. I think that perhaps you don't grasp how 
>> difficult it is to help without being able to access the simulation 
>> directly. Therefore we have ideas and we ask you to do specific things that 
>> are going to move us toward a solution, either by finding answers or by 
>> ruling out possibilities.
>>
>> It is actually useful information to know that "Sometimes it is the peptide 
>> N and H, like in the case of 981 and 982, and sometimes others" ... but when 
>> it seems like you don't want to provide the requested information my first 
>> inclination is to give up on trying to help.
>>
>> At this point, there are a few unanswered old questions and I have some new 
>> questions.
>>
>> 1. Can you reproduce this with a water box?
>
> The error is reproducible in a box of protein and water only.
>
>> 2. Can you reproduce this with your protein in vacuum?
>
> The error is reproduced in vacuum.
>
>> 3. If neither 2 or 3, then can you step slowly from one of these systems 
>> toward your final system and identify the point at which the lincs warnings 
>> arise?
>> 4. Do you get the warnings without Ca also, or just with Ca?
>
> I am not sure what this mean. I get this warning mainly for N-H, but also for 
> Ca-C, pairs of atoms
>
>> 5. Can you reproduce this with the SD integrator? If you are really against 
>> trying this, then at least can you reproduce this with a single Berendsen 
>> temperature coupling group?
>
> When I use SD integrator, the simulations run fine.
>
>> 6. Can you reproduce this without using the reaction field? Either with PME 
>> or a simple cutoff?
>
> Using PME the system is running just fine.
>
>> 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where 
>> you start to see this warning?
>
> I can't tell, 'cause I jump from 4.0.7 to 4.5.4.
>
> Thanks for the help,
> Itamar
>
>>
>> Chris.
>>
>> -- original message --
>>
>> Hi Justin,
>>
>> I did repeat it using gen_val and running temperature the same, with no 
>> effect, it is still crash. I didn't replied point #6 because the atoms which 
>> triggers the LINCS are different between each try. Sometimes it is the 
>> peptide N and H, like in the case of 981 and 982, and sometimes others. In 
>> addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 
>> I can find.
>>
>> Itamar
>>
>>
>> On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote:
>>
>>>
>>>
>>> Itamar Kass wrote:
 Hi Mark,
 I didn't had the time to do the SD yet, but serial run end with the same 
 results. I didn't try water only system, as this is of no interest to me, 
 but I will simplify the system later on.
>>>
>>> Being of interest to you and being a useful diagnostic may be different.  
>>> It's important to rule out different variables to arrive at a solution, 
>>> which I suspect is of interest to you.  You also haven't addressed points 
>>> #1 and #6 in Chris' message.
>>>
>>> -Justin
>>>
 Cheers,
 Itamar
 On 01/09/2011, at 10:51 AM, Mark Abraham wrote:
> On 1/09/2011 10:20 AM, Itamar Kass wrote:
>> Hi Chris,
>>
>> Thanks for the email, I am sorry it took me some time to replay. I tried 
>> 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and 
>> again the simulations had stopped after 1000 LINCS error (I can extend 
>> the simulations using 4.0.7).
>>
>> I know that gromacs stopped after 1000 LINCS, but this is usually a sign 
>> that something bad is going on in the system.
> OK. Chris suggested a number of other strategies that will help determine 
> which aspect of 4.5.4 is behaving differently. How did those strategies 
> work out?
>
> Mark
>
>> Cheers,
>> Itamar
>>
>> On 18/08/2011, at 12:03 PM, chris.neale at utoronto.ca wrote:
>>
>>> OK, here's my last few ideas:
>>>
>>> 1. Please try to repeat this with gen_vel set to the same value as your 
>>> temperat