[gmx-users] Re: genbox Not enough memory

[Dr. Vitaly Chaban]

On Thu, Oct 11, 2012 at 12:19 AM, Juliette N.  wrote:
> Hi,
>
> I will try to compress before doing genbox. As for the number of atoms, as I
> said I dont intend to fill up the whole box with solvent.



If you do not fill the whole box, it would be probably essentially the
same as if you have no solvent at all.

If you initially compress your polymer in a vacuum, perhaps, you will
get better outcome with a smaller time-step and higher pressure.

Good luck!

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark








So I put around
> 4000 solvent molecules to get the desired polymer Wt%, hence there would be
> a lot of free space for a total of 120 000 atoms approx..Also I tried - cs
> solvent.gro but it stucks and doest work.
>
> Thanks for the comments,
> J.
>
>
> On 10 October 2012 17:16, Dr. Vitaly Chaban  wrote:
>> By the way, if you place your solvent molecule (-cs .gro) into a
>> very large box, such as 10x10x10nm, genbox may perform well. I did NOT
>> try, just an idea.
>>
>> For the overall system setup, I would rather follow the previous
>> comments anyway.
>>
>>
>>
>> On Wed, Oct 10, 2012 at 10:49 PM, Dr. Vitaly Chaban 
>> wrote:
>>> On Wed, Oct 10, 2012 at 10:24 PM, Juliette N. 
>>> wrote:
 Hi again,

 The reason I have this big box is that I have fully extended chains of
 the length of ~ 250 nm,. In fact this 250 nm is the minimum size that
 I can fit the chain in the box; and I am going to fill this box with
 solvent and use NPT to increase the density. So I dont need to fill up
 the box with solvent entirely. The total number of atoms would be
 around 120 000.
>>>
>>>
>>> Sorry, I do not believe you. 120 000 atoms cannot ever fill the volume
>>> of 250*250*250 nm^3.
>>>
>>>
 I have access to a certain number of nodes. I am wondering if this
 "adding of memory" is merely a hardware issue or there is some other
 ways to get around this.?
>>>
>>> This "adding memory" is the appetit of the genbox in its current
>>> incarnation. I am sure that the developers did not expect to apply
>>> this utility for the systems larger than 30x30x30 nm. You can always
>>> construct a very simple script that puts your solvent evenly
>>> throughout the box.
>>>
>>> Why not to gently compress the box WITHOUT solvent. Unless you
>>> want to observe real-time folding of the polymer. It is probably not
>>> so good idea to start with a huge box and super low density.
>>>
>>>
>>> Dr. Vitaly V. Chaban
>>> MEMPHYS - Center for Biomembrane Physics
>>> Department of Physics, Chemistry and Pharmacy
>>> University of Southern Denmark
>>> Campusvej 55, 5230 Odense M, Denmark
>>>
>>>
>>>
>>>
>>>
>>>
 Thank you for your comments,


 On 10 October 2012 13:14, Dr. Vitaly Chaban  wrote:
>>
>> Thanks..You are right...The last line of gro file says 250 so it is in
>> nm!...
>>
>> On 10 October 2012 12:30, Christopher Neale
>>  wrote:
>>> Sounds like you ran out of memory. Many clusters have a few
>>> large-memory nodes. Can you use one of those?
>>> It's failing on a call for 1.3 Gb of memory, which by itself isn't
>>> really a lot...
>>>
>>> Also, can you confirm 250 A box length, not 250 nm box length?
>>> Gromacs defines length in units of nm.
>>>
>>> Chris.
>>>
>>> -- original message --
>>>
>>> I am trying to build a polymer in solvent system by solvating my
>>> fully
>>> extended polymer chains in a box of size 250 250 250 A. I am adding
>>> 4500 solvent molecules as below
>>>
>>>  genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500
>>>
>>> Adding solvents is a slow process and takes much time and at the end
>>> I get:
>>>
>>> Program genbox, VERSION 4.5.4
>>> Source code file: smalloc.c, line: 214
>>>
>>> Fatal error:
>>> Not enough memory. Failed to realloc 1338273212 bytes for grid->nra,
>>> grid->nra=0x0
>>> (called from file nsgrid.c, line 483)
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>> Is this happening because of the huge amount of free space to be
>>> filled with the solvent? Please help me.
>
>
> Genbox sometimes suffers from the out-of-memory error. Based on my own
> investigation, this is indeed what happens here, because the utility
> uses a kind of grid during its operation. The larger the cell, the
> more hungry it becomes, no matter how many molecules you want to
> insert. The standard advice therefore applies - add memory...
>
> Another question is why you need such a huge box? The only thing I
> could imaging is simulating a droplet-vapor/air interface...
>
> Another advice is to start with a s

[gmx-users] pull=constraint gives zero forces

[Thomas Schlesier]

See the SHAKE algorithm in the manual.
Especially equation (3.98)
-> G_i = \sum_k \lambda_k * (\partial \sigma_k)/(\partial r_i)
where G_i is the constraint force
\sigma_k are the equations for the constraints
and \lambda_k is the lagrange multiplier

'Understanding molecular simulation' (D. Frenkel, B. Smit)
gives these equations for bond-constraints as
\sigma = r_ij^2 - d_ij^2
where r_ij is the real distance, and d_ij to one to which one wants to 
constrain the bond length


from this \lambda_k would correspond to a force constant.

Greetings
Thomas


Am 10.10.2012 18:41, schrieb gmx-users-requ...@gromacs.org:

How can there be forces for holonomic constraints? Is this described by an 
equation in the manual?
Just because there are values in the pullf.xvg file does not mean that these 
values are forces.
If they are forces, what is the force constant and what is the equation that 
defines this force?

Thank you,
Chris.

-- original message --

But for GMX 4.0.7 there are forces in the pullf.xvg. The forces which
arise rom the contraint the hold the two groups fixed. I use them for
thermodynamic integration...

I use the following mdp-parameters, probably this gives you an idea what
you might make different:
; AFM OPTIONS
pull=  constraint
pull_geometry   =  distance
pull_dim=  Y Y Y
pull_start  =  yes
pull_nstfout=  10
pull_nstxout=  50
pull_ngroups=  1
pull_group0 =  REF
pull_group1 =  ZUG
pull_rate1  = 0.000
pull_init1  = 0.000
pull_constr_tol  = 1e-06

But as Chris said, better post the complete mdp-file (probably for both
GMX 4.0.7 and 4.5.x) so we can comment on them.

Grettings
Thomas


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Re: [gmx-users] Re: genbox Not enough memory

[Jochen Hub]

Hi,

this is due to the way genbox -ci is currently implemented. It calles 
add_conf() too often which leaks memory. So you'll have to edit the code.


Jochen


You'll have to edit the genbox code in order

Am 10/10/12 7:14 PM, schrieb Dr. Vitaly Chaban:


Thanks..You are right...The last line of gro file says 250 so it is in nm!...

On 10 October 2012 12:30, Christopher Neale
 wrote:

Sounds like you ran out of memory. Many clusters have a few large-memory nodes. 
Can you use one of those?
It's failing on a call for 1.3 Gb of memory, which by itself isn't really a 
lot...

Also, can you confirm 250 A box length, not 250 nm box length? Gromacs defines 
length in units of nm.

Chris.

-- original message --

I am trying to build a polymer in solvent system by solvating my fully
extended polymer chains in a box of size 250 250 250 A. I am adding
4500 solvent molecules as below

  genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500

Adding solvents is a slow process and takes much time and at the end I get:

Program genbox, VERSION 4.5.4
Source code file: smalloc.c, line: 214

Fatal error:
Not enough memory. Failed to realloc 1338273212 bytes for grid->nra,
grid->nra=0x0
(called from file nsgrid.c, line 483)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Is this happening because of the huge amount of free space to be
filled with the solvent? Please help me.



Genbox sometimes suffers from the out-of-memory error. Based on my own
investigation, this is indeed what happens here, because the utility
uses a kind of grid during its operation. The larger the cell, the
more hungry it becomes, no matter how many molecules you want to
insert. The standard advice therefore applies - add memory...

Another question is why you need such a huge box? The only thing I
could imaging is simulating a droplet-vapor/air interface...

Another advice is to start with a smaller box and then extend its
deminsions using editconf (which does not "care about the box size").


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark



--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

[Shima Arasteh]

Thanks for your explanation.

I'm doing protein insertion in lipid-membrane following Justin's tutorial 
steps, but My Protein and Lipid Membrane are different of KALP15 and DPPC. 

Now, when I visualized .gro file of last iteration in KALP15-DPPC ( the 
simulation what I did sometime ago to learn how protein insertion is ) I see 
the same problem here too. 
To use the position restrains, I added "define=-DSTRONG_POSRES" to the energy 
minimization .mdp file and then went through the iteration step.


Sincerely,
Shima


- Original Message -
From: Christopher Neale 
To: "gmx-users@gromacs.org" 
Cc: 
Sent: Wednesday, October 10, 2012 7:56 PM
Subject: [gmx-users] Secondary structure after InflateGRO step - protein in 
lipid membrane

Can you compute the Ca RMSD to the starting structure (using structural 
fitting) as a function of inflategro step 
and post it somewhere online and link it here? It is very difficult to know 
what is going on based simply on the 
fact that VMD doesn't render your protein as you expect it to.

Also, did you really follow that tutorial *exactly*, or did you substitute your 
own protein molecule. If you used
a different protein, I suggest that you go back and redo the tutorial with 
KALP15 and see if you have the
same problems. 

My guess is that you are not actually using position restraints, despite the 
fact that you intend to. To check this,
you can do a simulation of your protein in vacuum with and without position 
restraints and see if you are actually
getting a very low Ca RMSD when using position restraints. Note that the #ifdef 
statement in your .itp
file must match the define = -D statement in your .mdp file.

I don't know why you would need to go through more inflategro runs to get a 
proper protein structure.
Inflategro is designed to avoid perturbing your protein while it moves the 
lipids around.

Chris.

-- original message --


I exactly followed the steps in Justin's tutorial of KALP15-DPPC, so I applied 
position restrain to restrain the protein in the step before iteration.

It doesn't seem to be artifact, because when I select only the protein in VMD, 
I see a broken secondary structure.
Sometime ago, other gmx users suggested that when one is using inflategro, it's 
not expected the complete secondary structure and it's needed to go through the 
iteration. I did iteration but it's still as before.


Sincerely,
Shima


- Original Message -
From: Christopher Neale 
To: "gmx-users at gromacs.org" 
Cc: 
Sent: Wednesday, October 10, 2012 7:09 PM
Subject: [gmx-users] Secondary structure after InflateGRO step - protein in 
lipid membrane

What, precisely, do you mean the SS of the protein is still incomplete? When 
you use inflategro, the conformation of your 
protein is intended to remain as in your initial conformation. Did you forget 
to use position restraints
on your protein during the contraction steps ( 
http://www.csb.bit.uni-bonn.de/inflategro.html )?

If it is just a visualization artefact, then you should be able to select only 
the protein in VMD and it 
should display just fine.

Chris.

-- original message --

I'm doing the protein insertion into the lipid membrane. After shrinking for 30 
times, I visualized the system, but the secondary structure of protein is still 
incomplete . How come? I finished the InflateGRO step.

Thanks for your suggestions in advance.

Sincerely,
Shima

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protein in lipid membrane
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Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

[Shima Arasteh]

I visualized the last output mdrun of KALP15-DPPC simulation, the secondary 
structure of protein is complete and it seems OK. Can I trust on it and not 
care about the visualization of system after inflategro?




 
Sincerely,
Shima


- Original Message -
From: Shima Arasteh 
To: Discussion list for GROMACS users 
Cc: 
Sent: Thursday, October 11, 2012 12:36 PM
Subject: Re: [gmx-users] Secondary structure after InflateGRO step - protein in 
lipid membrane



Thanks for your explanation.

I'm doing protein insertion in lipid-membrane following Justin's tutorial 
steps, but My Protein and Lipid Membrane are different of KALP15 and DPPC. 

Now, when I visualized .gro file of last iteration in KALP15-DPPC ( the 
simulation what I did sometime ago to learn how protein insertion is ) I see 
the same problem here too. 
To use the position restrains, I added "define=-DSTRONG_POSRES" to the energy 
minimization .mdp file and then went through the iteration step.


Sincerely,
Shima


- Original Message -
From: Christopher Neale 
To: "gmx-users@gromacs.org" 
Cc: 
Sent: Wednesday, October 10, 2012 7:56 PM
Subject: [gmx-users] Secondary structure after InflateGRO step - protein in 
lipid membrane

Can you compute the Ca RMSD to the starting structure (using structural 
fitting) as a function of inflategro step 
and post it somewhere online and link it here? It is very difficult to know 
what is going on based simply on the 
fact that VMD doesn't render your protein as you expect it to.

Also, did you really follow that tutorial *exactly*, or did you substitute your 
own protein molecule. If you used
a different protein, I suggest that you go back and redo the tutorial with 
KALP15 and see if you have the
same problems. 

My guess is that you are not actually using position restraints, despite the 
fact that you intend to. To check this,
you can do a simulation of your protein in vacuum with and without position 
restraints and see if you are actually
getting a very low Ca RMSD when using position restraints. Note that the #ifdef 
statement in your .itp
file must match the define = -D statement in your .mdp file.

I don't know why you would need to go through more inflategro runs to get a 
proper protein structure.
Inflategro is designed to avoid perturbing your protein while it moves the 
lipids around.

Chris.

-- original message --


I exactly followed the steps in Justin's tutorial of KALP15-DPPC, so I applied 
position restrain to restrain the protein in the step before iteration.

It doesn't seem to be artifact, because when I select only the protein in VMD, 
I see a broken secondary structure.
Sometime ago, other gmx users suggested that when one is using inflategro, it's 
not expected the complete secondary structure and it's needed to go through the 
iteration. I did iteration but it's still as before.


Sincerely,
Shima


- Original Message -
From: Christopher Neale 
To: "gmx-users at gromacs.org" 
Cc: 
Sent: Wednesday, October 10, 2012 7:09 PM
Subject: [gmx-users] Secondary structure after InflateGRO step - protein in 
lipid membrane

What, precisely, do you mean the SS of the protein is still incomplete? When 
you use inflategro, the conformation of your 
protein is intended to remain as in your initial conformation. Did you forget 
to use position restraints
on your protein during the contraction steps ( 
http://www.csb.bit.uni-bonn.de/inflategro.html )?

If it is just a visualization artefact, then you should be able to select only 
the protein in VMD and it 
should display just fine.

Chris.

-- original message --

I'm doing the protein insertion into the lipid membrane. After shrinking for 30 
times, I visualized the system, but the secondary structure of protein is still 
incomplete . How come? I finished the InflateGRO step.

Thanks for your suggestions in advance.

Sincerely,
Shima

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Re: [gmx-users] .n2t file for the CHARMM forcefield

[Justin Lemkul]

On 10/10/12 11:27 PM, Elie M wrote:


Understandable. I meant the content of the .n2t file itself ; will it contain 
the same info as the OPLSAA with just changes in values according to the CHARMM 
field?


Yes.  File formats are always the same.

-Justin


Thank you
Elie


Date: Wed, 10 Oct 2012 23:13:34 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] .n2t file for the CHARMM forcefield



On 10/10/12 11:11 PM, Elie M wrote:


Ok. This means that I have to form the .n2t file for the CHARMM field as it is 
required by x2top. For the OPLSAA field the format was:
"Copls_1570.00012.011  4H 0.108   H 0.108   H 0.108   C 0.150C
opls_1580.000  12.0114H 0.108   H 0.108   C 0.150   C 
0.150"
How does this become in CHARMM? Shall we keep the atom names and change the 
oplsaa into atom types like CE1, CD,.and keep the rest fixed?



The charges will be different and perhaps the bond lengths will be different.

-Justin

--


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


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


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Re: [gmx-users] Confusion in passing check point file

[Justin Lemkul]

On 10/10/12 11:53 PM, Venkat Reddy wrote:

Dear all,
I am doing a protein-ligand simulation and following Justin's tutorials. I
have confusion in passing check point file to the next step in position
restrain simulation (during NPT). I am slowly releasing the restraints
during NPT simulation, *viz., 1000100.101noPR*. So, during
NPT-PR, is it required to pass the check-point file generated in the
previous step to the next step (100010010...1noPR)? or is it
fine if I use directly the check point file generated during NPT-no PR step
to final MD step?



You seem to be asking two questions, so it's not really a matter of "or."  One 
should always pass the final checkpoint of the previous stage of simulation to 
the current stage.  So during your reduction of restraints, you should pass the 
checkpoint from the previous restraint strength.  At the outset of MD, you 
should pass the checkpoint from whatever the step immediately prior to it was, 
which, from the description, is NPT in the absence of restraints.


-Justin

--


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


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Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

[Justin Lemkul]

On 10/11/12 5:57 AM, Shima Arasteh wrote:

I visualized the last output mdrun of KALP15-DPPC simulation, the secondary 
structure of protein is complete and it seems OK. Can I trust on it and not 
care about the visualization of system after inflategro?




That's probably a reasonable conclusion.  Sometimes visualization can be 
misleading.  What you should trust the most is the outcome of the EM during 
shrinking of InflateGRO and whether it generates sensible forces.


-Justin

--


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


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Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

[Shima Arasteh]

This is a sample of energy minimization, solvation and ion neutralization in my 
own system ( protein in POPC):

Steepest Descents converged to Fmax < 100 in 18240 steps
Potential Energy  = -1.0357691e+06
Maximum force =  8.0741402e+01 on atom 4716
Norm of force =  3.1694601e+00

I think it seems sensible, however I am not sure.



 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Thursday, October 11, 2012 2:21 PM
Subject: Re: [gmx-users] Secondary structure after InflateGRO step - protein in 
lipid membrane



On 10/11/12 5:57 AM, Shima Arasteh wrote:
> I visualized the last output mdrun of KALP15-DPPC simulation, the secondary 
> structure of protein is complete and it seems OK. Can I trust on it and not 
> care about the visualization of system after inflategro?
> 
> 

That's probably a reasonable conclusion.  Sometimes visualization can be 
misleading.  What you should trust the most is the outcome of the EM during 
shrinking of InflateGRO and whether it generates sensible forces.

-Justin

-- 

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Research Scientist
Department of Biochemistry
Virginia Tech
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Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

[Justin Lemkul]

On 10/11/12 7:27 AM, Shima Arasteh wrote:

This is a sample of energy minimization, solvation and ion neutralization in my 
own system ( protein in POPC):

Steepest Descents converged to Fmax < 100 in 18240 steps
Potential Energy  = -1.0357691e+06
Maximum force =  8.0741402e+01 on atom 4716
Norm of force =  3.1694601e+00

I think it seems sensible, however I am not sure.




Perfectly reasonable.  You achieved an Fmax below the desired value and its 
magnitude makes sense given the size of the system.


-Justin

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Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

[Shima Arasteh]

Thanks.
 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Thursday, October 11, 2012 3:00 PM
Subject: Re: [gmx-users] Secondary structure after InflateGRO step - protein in 
lipid membrane



On 10/11/12 7:27 AM, Shima Arasteh wrote:
> This is a sample of energy minimization, solvation and ion neutralization in 
> my own system ( protein in POPC):
>
> Steepest Descents converged to Fmax < 100 in 18240 steps
> Potential Energy  = -1.0357691e+06
> Maximum force     =  8.0741402e+01 on atom 4716
> Norm of force     =  3.1694601e+00
>
> I think it seems sensible, however I am not sure.
>
>

Perfectly reasonable.  You achieved an Fmax below the desired value and its 
magnitude makes sense given the size of the system.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Re: genbox Not enough memory

[Jochen Hub]

ps: There is a fix for this issue in Gerrit code review:

https://gerrit.gromacs.org/#/c/1175/

which introduces a fix genbox -allpair. This avoid the memory-leaky 
neighbor searching, which is the reason for your problem.


Jochen


Am 10/11/12 10:56 AM, schrieb Jochen Hub:

Hi,

this is due to the way genbox -ci is currently implemented. It calles
add_conf() too often which leaks memory. So you'll have to edit the code.

Jochen


You'll have to edit the genbox code in order

Am 10/10/12 7:14 PM, schrieb Dr. Vitaly Chaban:


Thanks..You are right...The last line of gro file says 250 so it is
in nm!...

On 10 October 2012 12:30, Christopher Neale
 wrote:

Sounds like you ran out of memory. Many clusters have a few
large-memory nodes. Can you use one of those?
It's failing on a call for 1.3 Gb of memory, which by itself isn't
really a lot...

Also, can you confirm 250 A box length, not 250 nm box length?
Gromacs defines length in units of nm.

Chris.

-- original message --

I am trying to build a polymer in solvent system by solvating my fully
extended polymer chains in a box of size 250 250 250 A. I am adding
4500 solvent molecules as below

  genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500

Adding solvents is a slow process and takes much time and at the end
I get:

Program genbox, VERSION 4.5.4
Source code file: smalloc.c, line: 214

Fatal error:
Not enough memory. Failed to realloc 1338273212 bytes for grid->nra,
grid->nra=0x0
(called from file nsgrid.c, line 483)
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

Is this happening because of the huge amount of free space to be
filled with the solvent? Please help me.



Genbox sometimes suffers from the out-of-memory error. Based on my own
investigation, this is indeed what happens here, because the utility
uses a kind of grid during its operation. The larger the cell, the
more hungry it becomes, no matter how many molecules you want to
insert. The standard advice therefore applies - add memory...

Another question is why you need such a huge box? The only thing I
could imaging is simulating a droplet-vapor/air interface...

Another advice is to start with a smaller box and then extend its
deminsions using editconf (which does not "care about the box size").


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark





--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
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Re: [gmx-users] Confusion in passing check point file

[Venkat Reddy]

Thanks Justin for the information. By the way, Could you please give me a
hint on the release of new GPU-version (4.6)?

On Thu, Oct 11, 2012 at 4:20 PM, Justin Lemkul  wrote:

>
>
> On 10/10/12 11:53 PM, Venkat Reddy wrote:
>
>> Dear all,
>> I am doing a protein-ligand simulation and following Justin's tutorials. I
>> have confusion in passing check point file to the next step in position
>> restrain simulation (during NPT). I am slowly releasing the restraints
>> during NPT simulation, *viz., 1000100.101**noPR*. So,
>> during
>>
>> NPT-PR, is it required to pass the check-point file generated in the
>> previous step to the next step (100010010...1**noPR)? or is
>> it
>> fine if I use directly the check point file generated during NPT-no PR
>> step
>> to final MD step?
>>
>>
> You seem to be asking two questions, so it's not really a matter of "or."
>  One should always pass the final checkpoint of the previous stage of
> simulation to the current stage.  So during your reduction of restraints,
> you should pass the checkpoint from the previous restraint strength.  At
> the outset of MD, you should pass the checkpoint from whatever the step
> immediately prior to it was, which, from the description, is NPT in the
> absence of restraints.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Confusion in passing check point file

[Justin Lemkul]

On 10/11/12 9:33 AM, Venkat Reddy wrote:

Thanks Justin for the information. By the way, Could you please give me a
hint on the release of new GPU-version (4.6)?



As I posted yesterday, I do not have any insight on a specific release date. 
It's close, but I'm not involved in any of the remaining coding that's going on.


-Justin


On Thu, Oct 11, 2012 at 4:20 PM, Justin Lemkul  wrote:




On 10/10/12 11:53 PM, Venkat Reddy wrote:


Dear all,
I am doing a protein-ligand simulation and following Justin's tutorials. I
have confusion in passing check point file to the next step in position
restrain simulation (during NPT). I am slowly releasing the restraints
during NPT simulation, *viz., 1000100.101**noPR*. So,
during

NPT-PR, is it required to pass the check-point file generated in the
previous step to the next step (100010010...1**noPR)? or is
it
fine if I use directly the check point file generated during NPT-no PR
step
to final MD step?



You seem to be asking two questions, so it's not really a matter of "or."
  One should always pass the final checkpoint of the previous stage of
simulation to the current stage.  So during your reduction of restraints,
you should pass the checkpoint from the previous restraint strength.  At
the outset of MD, you should pass the checkpoint from whatever the step
immediately prior to it was, which, from the description, is NPT in the
absence of restraints.

-Justin

--
==**==

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

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[gmx-users] Installing an Individual Tool (g_select)

[Smitty]

Dear Gromacs Guru's,

I currently have an old installation of gromacs (4.0.7) on my cluster and
the newer 4.5.4 on a gpu-machine that my group was using to explore the
gromacs-gpu acceleration. While using the newer version we found that
g_select was incredibly useful and seemed to work with both our 4.5.4
trajectories and our 4.0.7 trajectories, the problem being that we could
only use g_select on the gpu machine. So here's my question, what do I need
to compile just the g_select program from the 4.5.4 package onto the older
machine. We are currently in the middle of running some simulations using
the older version so replacing the entire gromacs package with the new
version is not an option.

Thanks for the help.

-Smitty



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Re: [gmx-users] Installing an Individual Tool (g_select)

[Erik Marklund]

Hi,

You don't have to replace existing installations. You can simply build a new 
gromacs version and install it in a different folder than your existing 
installation. If you still want only the g_select tool for whatever reason you 
can usually chose to only build one tool (and its dependencies)  by issuing 
"make g_select" (or whatever tool of your choice). Installing it, however, is 
more problematic iirc, but you can in fact run it from the build directory.

Best,

Erik

On 11 okt 2012, at 15.48, Smitty wrote:

> Dear Gromacs Guru's,
> 
> I currently have an old installation of gromacs (4.0.7) on my cluster and
> the newer 4.5.4 on a gpu-machine that my group was using to explore the
> gromacs-gpu acceleration. While using the newer version we found that
> g_select was incredibly useful and seemed to work with both our 4.5.4
> trajectories and our 4.0.7 trajectories, the problem being that we could
> only use g_select on the gpu machine. So here's my question, what do I need
> to compile just the g_select program from the 4.5.4 package onto the older
> machine. We are currently in the middle of running some simulations using
> the older version so replacing the entire gromacs package with the new
> version is not an option.
> 
> Thanks for the help.
> 
> -Smitty
> 
> 
> 
> --
> View this message in context: 
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phone:+46 18 471 6688fax: +46 18 511 755
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[gmx-users] Regarding Gromacs output files.

[R.Vidya Rajendran (10PHD013)]

Hello Friends,

I have two very specific queries regarding gromacs output files.

1) Since we can generate .xtc file during mdrun, Is is possible to
stop generating .trr files, because it used to be very huge and less
useful.

2) .xtc & .tpr files generated by gms4.5.5 version is not readable by
gms4.0.4, Is their any possibility to make readable ?


Thank you!


regards
Vidya
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Re: [gmx-users] Regarding Gromacs output files.

[Justin Lemkul]

On 10/11/12 10:17 AM, R.Vidya Rajendran (10PHD013) wrote:

Hello Friends,

I have two very specific queries regarding gromacs output files.

1) Since we can generate .xtc file during mdrun, Is is possible to
stop generating .trr files, because it used to be very huge and less
useful.



Set nstxout, nstvout, and nstfout to zero in the .mdp file.  This will suppress 
.trr output.



2) .xtc & .tpr files generated by gms4.5.5 version is not readable by
gms4.0.4, Is their any possibility to make readable ?



The .xtc file can be read, the problem is the .tpr file.  You would have to 
recreate it under version 4.0.4, which requires small topology modifications.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
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[gmx-users] error during minimization

[Shine A]

Sir,

   I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But during minimization getting error like this..

There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 18.5346 nm
   Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition

why it happens? can you give me a solution for this?
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Re: [gmx-users] Regarding Gromacs output files.

[Erik Marklund]

On 11 okt 2012, at 16.17, R.Vidya Rajendran (10PHD013) wrote:

> Hello Friends,
> 
> I have two very specific queries regarding gromacs output files.
> 
> 1) Since we can generate .xtc file during mdrun, Is is possible to
> stop generating .trr files, because it used to be very huge and less
> useful.
> 

"Less useful" depends on the application, but in many cases yes.

> 2) .xtc & .tpr files generated by gms4.5.5 version is not readable by
> gms4.0.4, Is their any possibility to make readable ?
> 

the xtc files are backwards-compatible I think.  You can generate a new tpr 
file with your older gromacs version using the same mdp input as for your 
existing tpr and use that in your analysis programs.

> 
> Thank you!
> 
> 
> regards
> Vidya
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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[gmx-users] Re: About Error in Equlibration while using CYC pdb

[Justin Lemkul]

Please keep the discussion on the mailing list.  I have told you several times 
that I do not reply to private Gromacs help requests unless I ask you to send me 
files for diagnostic purposes.  You stand a better chance of resolving the issue 
with the help of the community, and the resolution will (hopefully) serve as a 
helpful thread for others in the future.


On 10/11/12 10:04 AM, vidhya sankar wrote:

Dear Justin  Thank you for your previous reply  For remembrance I have pasted
Here your previous reply


You don't necessarily have to use LINCS, but constraints are commonly applied in
order to use longer timesteps, and rigid bonds are a better model of reality.
Simple visualization does not indicate that the topology is sound.  The fact
that your EM is insufficient and that the equilibration run fails instantly
indicates that the starting geometry, topology, or both, are problematic.  Based
on the available information, we can't tell what is the source of the problem.

I Have  attched   my Topology and Pdb  to your Mail Please Give Possible
suggestion and pint out error in topology and Pdb
Gromacs  Mailing List Does not allow any Attachemnt  so I have sent you to your
Mail  Regret me if you feel inconvenience



I'm not going to hunt through a 1100-line file and hope to figure out what 
you've done to try to make it work.  You need to describe precisely what 
modifications you have made, show any relevant snippets (which can be copied and 
pasted, rather than sending attachments).



then You Gave the HyperLink for Diagonastic steps
In That page They  told me To use g_energy tool. it Quoted that  Spiking of
intramolecular term   indicates improper bonded parameter
  What is the Meaning of the Above statement Viz Spiking ?


A spike is a sudden increase.


Also Which Term Should i select When i run g_energy tool To detect the spiking
of Intramolcular term either Bonded Parameter or Nonbonded Parameter



Any of the terms may be useful.  It's impossible to try to guess which one, if 
any, will reveal the source of the problem.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] error during minimization

[Justin Lemkul]

On 10/11/12 10:27 AM, Shine A wrote:

Sir,

I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But during minimization getting error like this..

 There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 18.5346 nm
Change the number of nodes or mdrun option -rdd
 Look in the log file for details on the domain decomposition

 why it happens? can you give me a solution for this?



http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

-Justin

--


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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] Regarding Gromacs output files.

[R.Vidya Rajendran (10PHD013)]

Hello Justin,

With regards to my second query ...to suppress the size of .trr I can
set nstxout, nstvout, and nstfout to zero in the .mdp file, But I am
afraid It will affect the .xtc file too.

regards
Vidya

On Thu, Oct 11, 2012 at 5:24 PM, Justin Lemkul  wrote:
>
>
> On 10/11/12 10:17 AM, R.Vidya Rajendran (10PHD013) wrote:
>>
>> Hello Friends,
>>
>> I have two very specific queries regarding gromacs output files.
>>
>> 1) Since we can generate .xtc file during mdrun, Is is possible to
>> stop generating .trr files, because it used to be very huge and less
>> useful.
>>
>
> Set nstxout, nstvout, and nstfout to zero in the .mdp file.  This will
> suppress .trr output.
>
>
>> 2) .xtc & .tpr files generated by gms4.5.5 version is not readable by
>> gms4.0.4, Is their any possibility to make readable ?
>>
>
> The .xtc file can be read, the problem is the .tpr file.  You would have to
> recreate it under version 4.0.4, which requires small topology
> modifications.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Regarding Gromacs output files.

[Justin Lemkul]

On 10/11/12 10:54 AM, R.Vidya Rajendran (10PHD013) wrote:

Hello Justin,

With regards to my second query ...to suppress the size of .trr I can
set nstxout, nstvout, and nstfout to zero in the .mdp file, But I am
afraid It will affect the .xtc file too.



It will not.  The frames in the .xtc file depend only on nstxtcout.  That is why 
there are separate keywords.


-Justin

--


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


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[gmx-users] about salt concentration

[Christopher Neale]

There are 4 reasons that I can think of:

A) Didn't consider it or know how to do it
B) Repeating a previous simulation (possibly with some modifications) -- e.g. 
simulation a protein in a lipid bilayer 
using lipid parameters that have been shown to give the desired area per lipid 
in the absence of salt but which 
have not been evaluated in the presence of salt.
C) No parameters for desired salts, such as the common phosphate buffered 
saline, in some force fields.
D) Trying to avoid unexpected and sometimes difficult to understand effects of 
salt binding to the protein, salt 
entry into a channel, etc. This is probably misguided because such things are 
possible once you have even a single
counter-ion, but it is the reason that I have avoided the use of excess salt in 
the past. However, in my more recent 
work I have started adding excess salt around the concentrations that you 
mention.

I'm sure that there are lots of other reasons.

Chris.

-- original message --

Dear GROMACS users,

In most of the papers that compare the results from MD with NMR data the
authors use just counter ions to neutralize the system. However, a salt
concentration of 0.10-0.15 M would be closer to the buffer solution used in
the NMR experiment. Why then people don't use more salt in their
simulations? Do they want to avoid ff inaccuracies or to be able to use a
shorter cutoff for the short range interactions? I would be very interested
to know the reason.

thanks,
Thomas

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[gmx-users] shell polarizable water model

[Ananya Mondal]

Hi Mikhail,
I am using GMX4.5.5 to simulate SWM4-NDP polarizable water model, it
is working fine.
When i am running separately NA+ polarizable ion in SWM4-NDP  water
and Cl- polarizable ion in SWM4-NDP polarizable water model, it is
working fine.
But when I use the both NA+ and CL- (NaCl salt solution) polarizable
model which is in conjuction with SWM4-NDP model, the RMS force is
very large:

can anyone give some idea, what i am missing..
Thanking you
Ananya

here is my itp file
[ defaults ]
LJ  Geometric
[ atomtypes ]
;namemass charge ptypec6c12
  WO15.99940   0.0 A 0.00.0
  WH 1.00800   0.0 A 0.00.0
  WS 0.0   0.0 S 0.00.0
  WD 0.0   0.0 D 0.00.0
  NAc   22.989769  0.0 A 0.00.0
  NAs0.000 0.0 S 0.00.0
  CLc   35.45300   0.0 A 0.00.0
  CLs0.000 0.0 S 0.00.0
[ nonbond_params ]
WO  WO  1  3.67796770E-03   3.83182123E-06
WO  NAc 1  7.84740725E-04   4.51332937E-07
WO  CLc 1  6.24036649E-03   1.83075990E-05
NAc NAc 1  1.56840324E-04   4.66461074E-08
CLc CLc 1  9.08923242E-03   6.44595639E-05
NAc CLc 1  1.46880350E-03   2.62418143E-06
[ moleculetype ]
; molname   nrexcl
SM2 2
[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   WO  1   SM2 OW1 1  1.71636
2   WH  1   SM2 HW2 1  0.55733
3   WH  1   SM2 HW3 1  0.55733
4   WD  1   SM2 DW  1 -1.11466
5   WS  1   SM2 SW  1 -1.71636
[ polarization ]
1   5   1   0.00097822
[ constraints ]
; i funct   doh dhh
1   2   1   0.09572
1   3   1   0.09572
3   2   1   0.15139
[ virtual_sites3 ]
4   1   2   3   2   0.5  0.024034
[ exclusions ]
; iatom excluded from interaction with i
1   2   3   4   5
2   1   3   4   5
3   1   2   4   5
4   1   2   3   5
5   1   2   3   4
[ moleculetype ]
; molname   nrexcl
NA+1
[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   NAc   1   NA NAc11.687597
2   NAs   1   NA NAs1   -0.687597
[ polarization ]
; See notes above.  alpha (nm^3)
1   2   1   0.000157
[ exclusions ]
; iatom excluded from interaction with i
1   2
2   1

[ moleculetype ]
; molname   nrexcl
Cl- 1

[ atoms ]
; idat type res nr  residu name at name cg nr   charge
1   CLc 1   ion CLc 12.457187
2   CLs 1   ion CLs 1   -3.457187

[ polarization ]
; See notes above.  alpha (nm^3)
1   2   1   0.003969

[ exclusions ]
; iatom excluded from interaction with i
1   2
2   1

here is my g.mdb file

include  =
define   =
integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 100
init_step= 0
simulation_part  = 1
comm-mode= Linear
nstcomm  = 10
comm-grps= system
bd-fric  = 0
ld-seed  = 1993
emtol= 0.1
emstep   = 0.01
niter= 30
fcstep   = 0
nstcgsteep   = 1000
nbfgscorr= 10
rtpi = 0.05
nstxout  = 10
nstvout  = 00
nstfout  = 0
nstlog   = 50
nstcalcenergy= -1
nstenergy= 10
nstxtcout= 250
xtc-precision= 1000
xtc-grps =
energygrps   = System
nstlist  = 5
ns-type  = grid
pbc  = xyz
rlist= 0.75
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 0.75
epsilon_r= 1
epsilon_rf   = 1
vdw-type = Cut-off
rvdw-switch  = 0
rvdw = 0.75
DispCorr = EnerPres
table-extension  = 1
energygrp_table  =
fourierspacing   = 0.12
fourier_nx   = 32
fourier_ny   = 32
fourier_nz   = 32
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no
gb_algorithm = Still
nstgbradii   = 0
rgbradii = 0
gb_saltconc  = 0
implicit_sol

Re: [gmx-users] about salt concentration

[Thomas Evangelidis]

Thanks Chris, very good points. I would like to add a potential drawback
for not using salt taken from my experience:

I simulated a coiled coil with one end having charge +12 and the other
zero. I ran a simulation with just 12 Cl- counter ions which tended to
cluster near the positively charged tail. In that simulation the
electrostatic potential in the box was uneven and that resulted to spurious
protein movement at the positively charged end.

I am now preparing a simulation with 0.15 M NaCl and zero net charge to see
the effect on protein dynamics. But I haven't seen many papers using excess
salt concentrations and that makes me worry about the validity of the
results I will get.

Thomas



On 11 October 2012 20:22, Christopher Neale wrote:

> There are 4 reasons that I can think of:
>
> A) Didn't consider it or know how to do it
> B) Repeating a previous simulation (possibly with some modifications) --
> e.g. simulation a protein in a lipid bilayer
> using lipid parameters that have been shown to give the desired area per
> lipid in the absence of salt but which
> have not been evaluated in the presence of salt.
> C) No parameters for desired salts, such as the common phosphate buffered
> saline, in some force fields.
> D) Trying to avoid unexpected and sometimes difficult to understand
> effects of salt binding to the protein, salt
> entry into a channel, etc. This is probably misguided because such things
> are possible once you have even a single
> counter-ion, but it is the reason that I have avoided the use of excess
> salt in the past. However, in my more recent
> work I have started adding excess salt around the concentrations that you
> mention.
>
> I'm sure that there are lots of other reasons.
>
> Chris.
>
> -- original message --
>
> Dear GROMACS users,
>
> In most of the papers that compare the results from MD with NMR data the
> authors use just counter ions to neutralize the system. However, a salt
> concentration of 0.10-0.15 M would be closer to the buffer solution used in
> the NMR experiment. Why then people don't use more salt in their
> simulations? Do they want to avoid ff inaccuracies or to be able to use a
> shorter cutoff for the short range interactions? I would be very interested
> to know the reason.
>
> thanks,
> Thomas
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 

==

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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[gmx-users] about salt concentration

[Christopher Neale]

What do you mean spurious protein movement?

Also, the instantaneous electrostatic potential is always uneven, and I am not 
sure why the average 
electrostatic potential would change with excess salt, excepting that I would 
expect it to converge more rapidly with excess salt.

Finally, if you are going to end up showing this comparison, it would be best 
if you ran 2 independent simulations 
of each salt concentration. Without repeats I often find the conclusions in 
such comparisons hard to pin down to 
the change in the system as opposed to statistical variation.

-- original message --

Thanks Chris, very good points. I would like to add a potential drawback
for not using salt taken from my experience:

I simulated a coiled coil with one end having charge +12 and the other
zero. I ran a simulation with just 12 Cl- counter ions which tended to
cluster near the positively charged tail. In that simulation the
electrostatic potential in the box was uneven and that resulted to spurious
protein movement at the positively charged end.

I am now preparing a simulation with 0.15 M NaCl and zero net charge to see
the effect on protein dynamics. But I haven't seen many papers using excess
salt concentrations and that makes me worry about the validity of the
results I will get.

Thomas
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[gmx-users] small tc-group

[fciocco]

Hi

I have a system with a lipid bilayer (128 phospolipids), aproximately 30 SOL
molecules per lipid, and a small highly charged peptide at certain distance
from the bilayer. I want to do a pulling simulation in order to pull the
peptide inside the membrane along the z-direction. So, taking into account
that I want to explore the differents configurations doing a serie of US
simulations, and that in some windows I have the peptide in the water bulk
and in others it is inside the hydrophobic core of the membrane (but with
some hydration water molecules), I'm wondering about what is the best
approach for define the tc-groups..?
Peptide Membrane SOL_Ions or Membrane Peptide_SOL_Ions ?
 
Note: when I choose the peptide separately, the temperature fluctuations are
high (between 50 and 100K approximately).  

any comment would be very appreciated.

best regards, Facundo 



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Re: [gmx-users] small tc-group

[Peter C. Lai]

I would couple it with the membrane to be honest. The point of the different
groups is to avoid the hot solvent cold solute sitution. Molecules with 
similar degrees of freedom have comparable heat capacities. Your small 
peptide is closer in size and bond layout to a lipid chain than to water.
The end state of the system also hase the peptide physically coupled to the
bilayer too, so Membrane_Peptide seems to be most consistent approach. 

On 2012-10-11 07:23:26PM -0700, fciocco wrote:
> Hi
> 
> I have a system with a lipid bilayer (128 phospolipids), aproximately 30 SOL
> molecules per lipid, and a small highly charged peptide at certain distance
> from the bilayer. I want to do a pulling simulation in order to pull the
> peptide inside the membrane along the z-direction. So, taking into account
> that I want to explore the differents configurations doing a serie of US
> simulations, and that in some windows I have the peptide in the water bulk
> and in others it is inside the hydrophobic core of the membrane (but with
> some hydration water molecules), I'm wondering about what is the best
> approach for define the tc-groups..?
> Peptide Membrane SOL_Ions or Membrane Peptide_SOL_Ions ?
>  
> Note: when I choose the peptide separately, the temperature fluctuations are
> high (between 50 and 100K approximately).  
> 
> any comment would be very appreciated.
> 
> best regards, Facundo 
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/small-tc-group-tp5001927.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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