[gmx-users] Reg:Usage of Walls

[vinothkumar mohanakrishnan]

Hi all

I have a question regarding the usage of walls. what for walls are used?
what difference does the presence of walls make in the simulation? kindly me
more specific (if possible explain it with an example). any help is highly
appreciated. it will be of great use for all the new users of Gromacs.

Regards
Vinoth
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[gmx-users] rotate a .xtc file?

[chris . neale]

Thanks Roland, I'll give it a shot.

Chris.


Hi,

since this is such a simple problem I suggest to simply write a program to
do it. I suggest to start with either the xdrfile library or with the the
template (available under share). My experience is writing those small
things myself is much faster than searching the net and asking on the list.

Roland

On Tue, Nov 2, 2010 at 11:30 PM,  wrote:

[Hide Quoted Text]
Dear users,

I have 100 GB of .xtc with 3E6 total frames that that I would like to
rotate by 90 deg about the z axis.

For a .gro file, I could do this with editconf. trjconv does not appear to
have this ability. Writing out so many frames as .gro just to rotate it with
editconf and turn it back into a .xtc seems like a slow idea. trjconv -fit
rotate will not work either since there is no way to predefine the angle of
rotation. Does anybody have any ideas?

I saw this:
http://www.mail-archive.com/gmx-users@gromacs.org/msg20311.html but no
reply.

Thanks,
Chris.


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Re: [gmx-users] Reg:walls and pbc xy

[vinothkumar mohanakrishnan]

Hi all

Can anyone help me out with the wall settings for running above mentioned
liquid-liquid interface. with the mdp file i have my system is exploding.
any help is highly appreciated.

Regards
Vinoth

On Tue, Nov 2, 2010 at 3:58 PM, vinothkumar mohanakrishnan <
kmvin...@gmail.com> wrote:

> Hi Berk
>
> Thank you. what settings i should change in mdp file (energy minimisation)
> to run the energy minimisation for the single liquid-liquid interface
> (liquid-vapour interface at the other two extremes) without any issues?
> kindly be specific ( what parameter i should change) below is my mdp file.
> any help is highly appreciated.
>
>
> integrator= steep
> emtol= 40.0
> emstep  = 0.01
> nsteps= 1
> nstxout= 100
> nstvout= 100
> nstfout= 100
> nstlog= 100
> nstenergy= 100
> nstlist= 5
> ns_type= grid
> rlist= 1.0
> coulombtype= PME
> rcoulomb= 1.0
> vdwtype= Cut-off
> rvdw= 1.0
> ewald_geometry= 3dc
> nwall= 2
> wall_type= 9-3
> wall_r_linpot= 1
> wall_atomtype   = opls_966 opls_968
> wall_density= 9-3 9-3
> wall_ewald_zfac= 3
> pbc= xy
> fourierspacing  = 0.18
>
> Regards
> Vinoth
>
> On Tue, Nov 2, 2010 at 3:41 PM, Berk Hess  wrote:
>
>>  I meant to say that if you see effects of one interface on another with a
>> layer of 1 nm thickness/height,
>> these effects will be less with a layer of 2 nm thickness and even less
>> with 10 nm thickness.
>>
>> Berk
>>
>> --
>> Date: Tue, 2 Nov 2010 15:30:34 +0530
>>
>> Subject: Re: [gmx-users] Reg:walls and pbc xy
>> From: kmvin...@gmail.com
>> To: gmx-users@gromacs.org
>>
>> Hi Berk
>>
>> Thank you once again. How can i use thick layers and what is the
>> procedure? can you explain it bit more on this?
>>
>> Regards
>> Vinoth
>>
>> On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess  wrote:
>>
>>  Hi,
>>
>> I have not heard about such issues, but it might depend a lot on your
>> particular application.
>> I would think you will always have disturbances, no matter if you use two
>> interfaces,
>> one interface with walls or one liquid-liquid interface and two
>> liquid-vapour interfaces.
>> The only solution to such problems is using thicker layers.
>>
>> The wall are on the bottom (z=0) and top (z=z_box) of the box, as the
>> manual says.
>>
>> Berk
>>
>> --
>> Date: Tue, 2 Nov 2010 14:59:31 +0530
>> Subject: Re: [gmx-users] Reg:walls and pbc xy
>>
>> From: kmvin...@gmail.com
>> To: gmx-users@gromacs.org
>>
>> Hi Berk
>>
>> I need only one interface because if i have two interfaces the "capillary
>> waves from one interface disturb the other even though the distance between
>> the average positions of the two interfaces are larger than the potential
>> cut-off" (this was said in the literature).
>>
>> Can anyone explain me why walls are used for interfaces? and what is the
>> purpose of using walls?.
>> suppose if i put nwall =2 where exactly are the walls created? can anyone
>> explain me with an example?
>>
>> i read the manual but it is not making any sense to me. if i know this i
>> know what correction i should make in my mdp file to make it work for pbc
>> xy. any help is highly appreciated.
>>
>> Regards
>> Vinoth
>>
>> On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess  wrote:
>>
>>  Hi,
>>
>> With wall_r_linpot your wall potential is linear from 1 nm downwards.
>> Since the LJ force is negative at 1 nm, your atoms are attracted to the
>> walls.
>>
>> But why not simply use two interfaces? You get double the sampling for
>> free
>> and you do not have to bother with complicated wall setups.
>>
>> Berk
>>
>> --
>> Date: Tue, 2 Nov 2010 11:49:48 +0530
>> From: kmvin...@gmail.com
>> To: gmx-users@gromacs.org
>> Subject: [gmx-users] Reg:walls and pbc xy
>>
>>
>> Hi Gromacians
>>
>> I want to create a liquid-liquid interface and study its properties. Hence
>> i combined two boxes ( say water and DCE). The two boxes  are well
>> equilibrated before merging and i created an interface. Now i want to
>> perform energy minimisation for the interface by appling pbc in the xy
>> direction and using walls. ( If i apply pbc in all the directions i get two
>> interfaces where as i need only one interface hence i am applying it only on
>> the xy direction and removing the boundary condition in the Z
>> direction.).When i performed the energy minimisation for the interfacial
>> system but i found that my system is exploding (several PDB files are
>> written while running mdrun is executed) and i dont know why?.There is no
>> issue when i use pbc in all directions. below is my em.mdp file. any help is
>> highly appreciated.
>>
>> integrator= steep
>> emtol= 40.0
>> emstep  = 0.01
>> nsteps= 1
>> nstxout= 100
>> nstvout= 100
>> nstfout= 100
>> nstlog= 100
>> nstenergy= 100
>> nstlist= 5

Re: [gmx-users] rotate a .xtc file?

[Roland Schulz]

Hi,

since this is such a simple problem I suggest to simply write a program to
do it. I suggest to start with either the xdrfile library or with the the
template (available under share). My experience is writing those small
things myself is much faster than searching the net and asking on the list.

Roland

On Tue, Nov 2, 2010 at 11:30 PM,  wrote:

> Dear users,
>
> I have 100 GB of .xtc with 3E6 total frames that that I would like to
> rotate by 90 deg about the z axis.
>
> For a .gro file, I could do this with editconf. trjconv does not appear to
> have this ability. Writing out so many frames as .gro just to rotate it with
> editconf and turn it back into a .xtc seems like a slow idea. trjconv -fit
> rotate will not work either since there is no way to predefine the angle of
> rotation. Does anybody have any ideas?
>
> I saw this:
> http://www.mail-archive.com/gmx-users@gromacs.org/msg20311.html but no
> reply.
>
> Thanks,
> Chris.
>
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>


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[gmx-users] rotate a .xtc file?

[chris . neale]

Dear users,

I have 100 GB of .xtc with 3E6 total frames that that I would like to  
rotate by 90 deg about the z axis.


For a .gro file, I could do this with editconf. trjconv does not  
appear to have this ability. Writing out so many frames as .gro just  
to rotate it with editconf and turn it back into a .xtc seems like a  
slow idea. trjconv -fit rotate will not work either since there is no  
way to predefine the angle of rotation. Does anybody have any ideas?


I saw this:  
http://www.mail-archive.com/gmx-users@gromacs.org/msg20311.html but no  
reply.


Thanks,
Chris.

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[gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?

[Chih-Ying Lin]

Hi
I read some papers and many simulations were performed under high
temperature to induce the unfolded protein.
However, the authors did not mention how they conducted the simulations
under high temperature, 498 K.
They did not mention which NVT or NPT were adopted for such high
temperature.
None of any parameters about the temperature coupling and pressure coupling
were described on the papers.


Are there any standard procedures to perform High temperature - MD
simulation?
Where can I find the standard procedures?


At 498K, protein is cooked.
Under NPT, the water evaporated. => so,  turn on pressure coupling with a
(very) high pressure to keep the water molecules.
Under NVT, the pressure increased dramatically.
So, to run MD simulations under the high temperature means to run the MD
simulation under high pressure at the same time?



But, I did read one paper that the authors performed the MD simulation under
high temperature and high pressures separately
and further discuss the effect the high temperature and the high pressures
on protein separately.



Thank you
Lin
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Re: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

[Rossen Apostolov]

Hi,

On 11/2/10 1:35 PM, Sander Pronk wrote:

Hi Michael,

I've just committed a fix to the git repository (it's in the 
release-4-5-patches branch)

There were 2 problems
- Energy files in double precision couldn't be read in 4.5.2, due to an overly 
strict error checking issue.
- The box matrix wasn't written out correctly (in any 4.5 version).

As Berk said, these issues are bad enough for a new version to be released soon.



We'll have one next Monday then!

Rossen


Sander


On 2 Nov 2010, at 11:55 , Michael Brunsteiner wrote:


Sander pronk wrote:



Hi Michael,

I've been able to reproduce both problems - I'll fix them shortly.

thanks for your swift reply!

I assume any fix will be in the Git version only for some time
to come, right?

cheers,
Michael



Sander


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RE: [gmx-users] Re: pressure of the liquid in NPT and NVT

[Dallas Warren]

What is the volume fluctuation like just prior to the end of the
previous run (NPT) that is used as the starting point for the NVT run?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 
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[gmx-users] Re: pressure of the liquid in NPT and NVT

[Vitaly Chaban]

> Unless the box was equilibrated at NPT at the start of the NPT run, or the
> run was very long, the average value over the whole run is not all that
> likely to be one from the equilibrium range. Take the last frame.

The system is pretty equilibrated. Just look at the energy drift - it
is negligible.
\
> We had a thread about this last week, and numerous more in the past. These
> observations are strongly dependent on the length of time over which you
> observe the average pressure, and the size of the system. Note that your
> fluctuations dwarf your average... See
> http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling

Yes, we had such discussions, but the main question is if this is
possible to get the same average pressure using NVT as I had in the
NPT. If no, I am just curious about the physical background of this
fact.

I believe, the average value should make sense. In the present case
the simulation time is 1 ns and the number of waters is 1728. I used
shorter intervals within this run and the pressure values (average, of
course) were always between -10 and -20 bar.

Vitaly
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Re: [gmx-users] pressure of the liquid in NPT and NVT

[Mark Abraham]

- Original Message -
From: Vitaly Chaban 
Date: Wednesday, November 3, 2010 6:10
Subject: [gmx-users] pressure of the liquid in NPT and NVT
To: gmx-users@gromacs.org

> Hi all,
> 
> Please suggest me what is the reason for the below situation.
> 
> The 1728 TIP4P waters system was simulated in NPT under 1bar
> maintained with Parrinello-Rahman barostat at 300K. Some results are
> below:
> 
> Energy  Average   RMSD Fluct.  Drift  
> Tot-Drift
> -
> --
> Total 
> Energy   -58121.6344.637344.476   0.18254936.5101
> Temperature 299.9134.11684 4.1138 0.00274337   
> 0.548679
> Pressure 
> (bar)  1.39811326.506317.633   -1.30948 -261.9
> Box-
> X   3.74431 0.00844567 0.00843154 -8.45584e-06
> -0.00169118
> Density 
> (SI)984.7686.664316.65307  0.00670051.34011
> 
> ==
> 
> The density is stable and the system looks like equilibrated one.
> 
> The output GRO was then renamed to conf.gro and the average Box-
> X from
> the previous run was set as the cubic box side length. 

Unless the box was equilibrated at NPT at the start of the NPT run, or the run 
was very long, the average value over the whole run is not all that likely to 
be one from the equilibrium range. Take the last frame.

> The barostat
> was switched off with no other changes in MDP. The same 
> properties for
> NVT are below:
> 
> Energy  Average   RMSD Fluct.  Drift  
> Tot-Drift
> -
> --
> Total 
> Energy   -58075.8309.575308.343  -0.477939   -95.5887
> Temperature 299.9164.089014.08678 -0.00233712  
> -0.467428
> Pressure 
> (bar) -18.5469286.376285.5740.3708174.1628
> 
> 
> So the pressure in NPT is ~1.4 and in NVT is ~(-19). How to 
> explain so
> big difference in average values? Is it possible to get a value of
> around 1 in the NVT?

We had a thread about this last week, and numerous more in the past. These 
observations are strongly dependent on the length of time over which you 
observe the average pressure, and the size of the system. Note that your 
fluctuations dwarf your average... See 
http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling

Mark

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Re: [gmx-users] g_hbond

[Erik Marklund]

Erik Marklund skrev 2010-11-02 20.33:

Carla Jamous skrev 2010-11-02 17.35:

Hi to all,

I'm sorry I'm asking again a question I asked a week ago but I still 
haven't found my answer:


I concatenated 3 trajectories of 3 different molecules (that have the 
same number of atoms) with trjcat: trjcat -settime


Then I ran g_hbond on the concatenated trajectory, I got an index.ndx 
file that contains an H-bond between the Thr121 of my protein and an 
atom N2 of my ligand. This H_bond  figures in the 3 trajectories when 
I look at the hbmap of my concatenated trajectory.


On the other hand, I ran g_hbond on each of the 3 different 
trajectories. This H_bond doesn't exist in the index files of two of 
my trajectories. So it doesn't match the result I get with my 
concatenated trajectory.


To be sure that this result is right, I calculated the angle and the 
r of my H-bond in VMD during each of the 3 trajectories and the 
results indicate that this H-bond doesn't exist (I consider that r 
must be < or equal to 0.35 nm and angle < or equal to 30 degrees).


Please can anyone tell me why the results of g_hbond in my 
concatenated trajectory don't match the results of g_hbond on each of 
my trajectories?


Thank you

Carla

Hi,

This sounds strange. Could you file a bugzilla and either upload the 
trajectories+tpr, or, if the files are huge, make them available my 
other means? I need to have a closer look, perhaps through a debugger.


A simple test you could do yourself is to make index groups containing 
only the atoms involved in that hbond and run g_hbond again. If the 
problem persists, then it looks like a bug. If not, then I still can't 
rule out misinterpretation of the matrix.


Erik

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---
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] g_hbond

[Erik Marklund]

Carla Jamous skrev 2010-11-02 17.35:

Hi to all,

I'm sorry I'm asking again a question I asked a week ago but I still 
haven't found my answer:


I concatenated 3 trajectories of 3 different molecules (that have the 
same number of atoms) with trjcat: trjcat -settime


Then I ran g_hbond on the concatenated trajectory, I got an index.ndx 
file that contains an H-bond between the Thr121 of my protein and an 
atom N2 of my ligand. This H_bond  figures in the 3 trajectories when 
I look at the hbmap of my concatenated trajectory.


On the other hand, I ran g_hbond on each of the 3 different 
trajectories. This H_bond doesn't exist in the index files of two of 
my trajectories. So it doesn't match the result I get with my 
concatenated trajectory.


To be sure that this result is right, I calculated the angle and the r 
of my H-bond in VMD during each of the 3 trajectories and the results 
indicate that this H-bond doesn't exist (I consider that r must be < 
or equal to 0.35 nm and angle < or equal to 30 degrees).


Please can anyone tell me why the results of g_hbond in my 
concatenated trajectory don't match the results of g_hbond on each of 
my trajectories?


Thank you

Carla

Hi,

This sounds strange. Could you file a bugzilla and either upload the 
trajectories+tpr, or, if the files are huge, make them available my 
other means? I need to have a closer look, perhaps through a debugger.


--
---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] pressure of the liquid in NPT and NVT

[Vitaly Chaban]

Hi all,

Please suggest me what is the reason for the below situation.

The 1728 TIP4P waters system was simulated in NPT under 1bar
maintained with Parrinello-Rahman barostat at 300K. Some results are
below:

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Total Energy   -58121.6344.637344.476   0.18254936.5101
Temperature 299.9134.11684 4.1138 0.00274337   0.548679
Pressure (bar)  1.39811326.506317.633   -1.30948 -261.9
Box-X   3.74431 0.00844567 0.00843154 -8.45584e-06
-0.00169118
Density (SI)984.7686.664316.65307  0.00670051.34011

==

The density is stable and the system looks like equilibrated one.

The output GRO was then renamed to conf.gro and the average Box-X from
the previous run was set as the cubic box side length. The barostat
was switched off with no other changes in MDP. The same properties for
NVT are below:

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Total Energy   -58075.8309.575308.343  -0.477939   -95.5887
Temperature 299.9164.089014.08678 -0.00233712  -0.467428
Pressure (bar) -18.5469286.376285.5740.3708174.1628


So the pressure in NPT is ~1.4 and in NVT is ~(-19). How to explain so
big difference in average values? Is it possible to get a value of
around 1 in the NVT?

Thank you.
Vitaly
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[gmx-users] Principal axis (g_principal)

[chris . neale]

Dear Sarah,

I just ran into the same thing so I'm posting this as a very late  
response to your querry.


I think that g_principal prints the transpose of the principal axes  
matrix, which is the exact opposite of what one would expect.


(1) First, I define a system that is longest in Z, second longest in  
Y, and shortest in X:


cne...@iram:~$ cat a.gro
a
12
1CL- CL1   0.000   0.000   0.000
2CL- CL2   0.000   1.000   0.000
3CL- CL3   0.000   2.000   0.000
4CL- CL4   1.000   0.000   0.000
5CL- CL5   1.000   1.000   0.000
6CL- CL6   1.000   2.000   0.000
7CL- CL7   0.000   0.000  10.000
8CL- CL8   0.000   1.000  10.000
9CL- CL9   0.000   2.000  10.000
   10CL- CL   10   1.000   0.000  10.000
   11CL- CL   11   1.000   1.000  10.000
   12CL- CL   12   1.000   2.000  10.000
50 50 50
cne...@iram:~$ cat a.top
#include "ffoplsaa.itp"
#include "ions.itp"


[ system ]
; name
grid


[ molecules ]
; namenumber
CL-  12



(2) Next I calculate the principal axes:


$ echo 0 |g_principal -f a.gro -s a.tpr >/dev/null 2>&1; cat axis1.dat  
axis2.dat axis3.dat

   0.000.00 0.00 1.00
   0.000.00 1.00 0.00
   0.001.00 0.00 0.00



(3) Finally, I rotate it by 90 deg and calculate the principal axes:

$ editconf -f a.gro -o b.gro -rotate 90 0 0 >/dev/null 2>&1; echo 0  
|g_principal -f b.gro -s a.tpr >/dev/null 2>&1; cat axis1.dat  
axis2.dat axis3.dat

   0.000.00 0.00 1.00
   0.001.00 0.00 0.00
   0.000.00 1.00 0.00



(4) I use VMD to confirm that the longest axis is in Y. Thus one must  
read the columns in axis1.dat as time1, X1, X2, X3 whereas one would  
intuit that they read as time1, X1, Y1, Z1.


I didn't test this extensively, but if my colleague determines that I  
am incorrect in what I have posted here then I will post that to this  
list.


If I am correct, then it would be very useful to get some #titles in  
the axisN.dat output files from g_principal.


Chris.


Dear gmx users,

I am doing several analyses (version 4.0.4) on my simulations with small
organic molecules inserting into a DMPC bilayer. Now I would like to calculate
whether the small molecule inserts into the membrane with a specific angle to
the membrane normal (or z-axis). I have used two approaches:

1) My molecule is a cyclohexene ring with two "para" substituents. I made an
index group with carbon number 3 and number 10 (in different groups) which
corresponds to the first substituent-atoms on each side of the ring. This
vector describes the shape of the molecule quite well. I then used g_bundle to
calculate the angle between this vector and the z-axis by echoing first the
C3-group and then the C10-group:

echo 0 1 | g_bundle -f xxx.xtc -s xxx.tpr -n xxx-vector.ndx -na 1 -z -ot
xxx-vector.xvg

This gives fairly reasonable results and angle distribution.

2) I also calculated the principal axis by g_principal where I echoed each
small molecule as a whole:

echo 0 | g_principal -f xxx.xtc -s xxx-1.tpr -n xxx-lim.ndx -a1
xxx-principal.dat -a2 xxx-axis2.dat -a3 xxx-axis3.dat

To get the angle between the principal axis and the z-axis one takes the arcos
the the z-component. This created quite a different and very broad angle
distribution.



This puzzled me very much since the difference between the C3-C10 vector and
the principal axis should not be that great.

I then used a small python program to calculate the principal axis of my
molecule and the result was again quite different than from  
g_principal. I have

tried to rotate each of my substituent groups by 120 degrees (creating 9
different conformations) and then calculate the difference in the principal
axis but this creates only a deviation of max. 16-17 degrees not at all
accounting for the very different angle distributions seen. I have not  
included

numbers but I can do so along with the python code. I would like to ask if
anyone can see any obvious mistakes or know of something special to be  
aware of

when using g_principal?



Thank you,

Sarah



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[gmx-users] g_hbond

[Carla Jamous]

Hi to all,

I'm sorry I'm asking again a question I asked a week ago but I still haven't
found my answer:

I concatenated 3 trajectories of 3 different molecules (that have the same
number of atoms) with trjcat: trjcat -settime

Then I ran g_hbond on the concatenated trajectory, I got an index.ndx file
that contains an H-bond between the Thr121 of my protein and an atom N2 of
my ligand. This H_bond  figures in the 3 trajectories when I look at the
hbmap of my concatenated trajectory.

On the other hand, I ran g_hbond on each of the 3 different trajectories.
This H_bond doesn't exist in the index files of two of my trajectories. So
it doesn't match the result I get with my concatenated trajectory.

To be sure that this result is right, I calculated the angle and the r of my
H-bond in VMD during each of the 3 trajectories and the results indicate
that this H-bond doesn't exist (I consider that r must be < or equal to 0.35
nm and angle < or equal to 30 degrees).

Please can anyone tell me why the results of g_hbond in my concatenated
trajectory don't match the results of g_hbond on each of my trajectories?

Thank you

Carla
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[gmx-users] (no subject)

[Green]

Dear gmx-users,

I have a rather elementary question regarding the value of box vectors when
invoked by g_energy.
If I am shearing a system using deform option, what does exactly, say,
"Box-XY" represent? Thanks,

gc
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[gmx-users] Update: (Problem Solved) -- Job crash: checkpoint file

[Shi, Chuanyin]

Thanks to our HPC support team who solved my problem.
They did something to my account and now I am able to run large replica 
exchange jobs.
I don't know whether this is really related to disk quota or special permission.
But for anyone who encountered this type of problem,
you can try running the job from home directory.
If this works, then you need to contact the administrator to remove the 
limitation on scratch space.


Chuanyin Shi
Department of Chemistry & Biochemistry
University of Oklahoma
Email: c...@ou.edu

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Shi, Chuanyin [c...@ou.edu]
Sent: Monday, October 25, 2010 11:37 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Job crash: checkpoint file

I wish the error would come from the quota.
But the disk quota is fine, we still have 2.0TB on the scratch space which is 
shared by everyone.
And I have other jobs running and no problem with writing outputs.
I've tried smaller REMD jobs on the cluster using only 1 node (8 cpus) and 
seems to be no problem.
But using 7 nodes and one (or two) node complains about that.
And several weird files are generated: mdrun_mpi.80s-12939,v002.local.btr, 
mdrun_mpi.80s-12940,v002.local.btr, 
v002 is the name of the node.


Chuanyin Shi
Department of Chemistry & Biochemistry
University of Oklahoma
Email: c...@ou.edu

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of David van der Spoel [sp...@xray.bmc.uu.se]
Sent: Monday, October 25, 2010 11:21 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Job crash: checkpoint file

On 2010-10-25 17.58, Shi, Chuanyin wrote:
> I am having exactly the same problem recently.
> The replica exchange job stops around 11000 steps.
> Switch to another cluster and the job is running fine.
> I wonder how often you've seen this type of crashing and any solutions for 
> this?
> Thanks.

Have you checked your quota?
I had the same problem recently, and I was indeed out of quota.
>
>
>
> Chuanyin Shi
> Department of Chemistry&  Biochemistry
> University of Oklahoma
> Email: c...@ou.edu
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Friday, October 08, 2010 1:19 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Job crash: checkpoint file
>
> Jianhui Tian wrote:
>> Dear GMX users,
>>
>> I am running a replica simulation and the job crashed with the following
>> message:
>>
>> File input/output error:
>> Cannot rename checkpoint file; maybe you are out of quota?
>>
>>   From the mailling list, I see this might be a permission problem.
>> However, I checked the file permission and nothing wrong was noticed.
>> If I rerun the crashed simulation, it goes through the second time. This
>> seems strong. Any suggestion is welcomed.
>>
>
> I've seen this happen when our filesystem blips.  It seems like you're able to
> run your job, so I don't think there's anything to do about it, except perhaps
> inquire with your sysadmins about the stability of the filesystem, and whether
> or not you can expect to have this happen frequently.
>
> -Justin
>
>> JH
>>
>
> --
> 
>
> 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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--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Can't pos

Re: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

[Sander Pronk]

Hi Michael,

I've just committed a fix to the git repository (it's in the 
release-4-5-patches branch)

There were 2 problems 
- Energy files in double precision couldn't be read in 4.5.2, due to an overly 
strict error checking issue.
- The box matrix wasn't written out correctly (in any 4.5 version). 

As Berk said, these issues are bad enough for a new version to be released soon.

Sander


On 2 Nov 2010, at 11:55 , Michael Brunsteiner wrote:

> 
> Sander pronk wrote:
> 
> 
>> Hi Michael,
>> 
>> I've been able to reproduce both problems - I'll fix them shortly.
> 
> thanks for your swift reply!
> 
> I assume any fix will be in the Git version only for some time
> to come, right?
> 
> cheers,
> Michael
> 
> 
>> Sander
> 
> 
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RE: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

[Berk Hess]

Well, it seems that any double precision energy file can not be read by 4.5.1 
or 4.5.2 code.
This is such a serious issue that we should bring out 4.5.3 within a week.

If you only need the box, g_traj can produce that.
If you need other energies you can use a 4.5.1 g_energy for the moment.

Berk

> Date: Tue, 2 Nov 2010 11:55:34 +0100
> From: michael.brunstei...@tugraz.at
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2
> 
> 
> Sander pronk wrote:
> 
> 
> >  Hi Michael,
> >
> >  I've been able to reproduce both problems - I'll fix them shortly.
> 
> thanks for your swift reply!
> 
> I assume any fix will be in the Git version only for some time
> to come, right?
> 
> cheers,
> Michael
> 
> 
> >  Sander
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8

[Mark Abraham]

On 2/11/2010 9:28 PM, Amin Arabbagheri wrote:


Hi Mark,

Are there differences between functions 9 and 1? So can I implement 
these dihedrals in successive lines, just using function 9 or 1?




Please read the dihedral manual sections in chapter 4 and 5 and have a 
look at (e.g.) some examples in the AMBER FF files.


Mark


Amin
--- On *Tue, 2/11/10, gmx-users-requ...@gromacs.org 
//* wrote:



From: gmx-users-requ...@gromacs.org 
Subject: gmx-users Digest, Vol 79, Issue 8
To: gmx-users@gromacs.org
Date: Tuesday, 2 November, 2010, 5:29

Send gmx-users mailing list submissions to
gmx-users@gromacs.org 

To subscribe or unsubscribe via the World Wide Web, visit
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. Re: multiple torsions for one dihedral (Mark Abraham)
   2. questions about umbrella sampling (mirc...@sjtu.edu.cn
)
   3. RE: Reg:walls and pbc xy (Berk Hess)
   4. Re: Reg:walls and pbc xy (vinothkumar mohanakrishnan)


--

Message: 1
Date: Tue, 02 Nov 2010 17:21:29 +1100
From: Mark Abraham >
Subject: Re: [gmx-users] multiple torsions for one dihedral
To: Discussion list for GROMACS users >
Message-ID: >
Content-Type: text/plain; charset="us-ascii"

Yes, multiple "type 1" dihedrals for use with AMBER and CHARMM
forcefields can be implemented, either as successive
[dihedraltypes] of type 9 (since GROMACS 4.0, IIRC) or as multiple
[dihedrals] of type 1 (since ages).

Mark

- Original Message -
From: Amin Arabbagheri >
Date: Tuesday, November 2, 2010 17:06
Subject: [gmx-users] multiple torsions for one dihedral
To: gmx-users@gromacs.org 

---
| > Hi all,
>
> I'm using AMBER99p force field in GROMACS. In the AMBER
forcefield for some dihedrals, there are several values, in which
n values are different.
> As an example, for C3-C3-N-C, I have
> C3-C3-N-C   .50  180.0  -4
> C3-C3-N-C   .15  180.0  -3
> C3-C3-N-C   .53  0.0   1
>
> For the version 4, is there a convenient way to use these
multiple  dihedrals?
> Thanks,
> Amin
>
|
---
>
> --
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Message: 2
Date: Tue, 02 Nov 2010 15:16:55 +0800
From: mirc...@sjtu.edu.cn 
Subject: [gmx-users] questions about umbrella sampling
To: gmx-users@gromacs.org 
Message-ID: <20101102151655.msoayn0bno4gk...@webmail.sjtu.edu.cn
>
Content-Type: text/plain;charset=GB2312;DelSp="Yes";   
format="flowed"


Dear All:

I am using umbrella sampling method to calculate potential of mean
force and I encountered the following questions:
1, at the *.ppa file, I need to incorporate a parameter indicating the
"the position of the pull group will restraint to, relative to the
reference group" (i.e., the "pos1" parameter).

To my understanding, in the initial structure, the pull group is not
need to at the exact position defined by the aformationed parameter
("pos1" parameter) in the .ppa file. I just need to put the pull group
near that position, am I right?

2, Since I need to define the position of the pull group relative to
the reference group. I need to calculate the mass center of the
reference group as well as that of the pull group. Does there any
tools in GROMACS to calculate their mass center?

Thank you very much for your time and your kindness!

Best Regards

R-X Gu



- 完成转寄邮件 -




--

Message: 3
Date: Tue, 2 Nov 2010 09:07:19 +0100
From: Ber

[gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

[Michael Brunsteiner]

Sander pronk wrote:



 Hi Michael,

 I've been able to reproduce both problems - I'll fix them shortly.


thanks for your swift reply!

I assume any fix will be in the Git version only for some time
to come, right?

cheers,
Michael



 Sander



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Re: [gmx-users] g_energy problem with 4.5.1 and 4.5.2

[Sander Pronk]

Hi Michael,

I've been able to reproduce both problems - I'll fix them shortly.

Sander


On 2 Nov 2010, at 10:28 , Michael Brunsteiner wrote:

> 
> Hi everybody,
> 
> I run NPT simulations (with the double precision version of mdrun) of a 
> polymer melt
> with anisotropic pressure scaling The simulation seems to go fine, and the
> trajectories look reasonable, but there's something wrong with my g_energy 
> output.
> 
> === With 4.5.1 I get weird values for the box dimensions.
> The g_energy output gives me something like:
> 
> Box-XX  4.7
> Box-YX  0.2
> Box-YY  5.5
> Box-ZX  0.0
> Box-ZY  0.0
> Box-ZZ  0.0
> 
> Mind you This is NOT because the box shrinks so much as both the input and
> output structures are roughly cubic with about 5 nm side-length, also if these
> values were true at least one box length would be shorter than the cut-off and
> I'd get a fatal error (which i don't). That is the values reported by 
> g_energy are
> wrong.
> For the same system with isotropic pressure scaling there's no problem.
> 
> === If I use g_energy and mdrun versions 4.5.2 then g_energy stops working
> altogether, I get:
> 
> prompt> g_energy_d -f ener.edr -o test.xvg -s topol.tpr
> 
> "Fatal error:
> edr file with negative step number or unreasonable time (and without version 
> number).
> If you want to use the correct frames before the corrupted frame and avoid 
> this fatal error set the env.var. GMX_ENX_NO_FATAL"
> 
> I tried both:
> prompt> export GMX_ENX_NO_FATAL=1
> or
> prompt> export GMX_ENX_NO_FATAL=1
> 
> in both cases I just get:
> 
> "File input/output error:
> Cannot read energy file header. Corrupt file?"
> 
> This I get with g_energy 4.5.2 for output from both mdrun 4.5.1 AND 4.5.2.
> 
> mdp file and sys info included below.
> 
> thanks for any feedback!
> 
> Michael
> 
> ==
> 
> My system:
> 
> Linux 2.6.32-5-amd64,
> gcc 4.4.5
> GNU C Library (Debian EGLIBC 2.11.2-6+squeeze1) stable release version 2.11.2
> CPU: Intel(R) Core(TM) i7 CPU 960 @ 3.20GHz
> 
> 
> the mdp file:
> 
> integrator   = md
> nsteps   = 25
> dt   = 0.002
> ;
> nstxtcout= 0
> nstenergy= 108
> nst_log  = 100
> nstxout  = 250
> nstvout  = 0
> energygrps   = ste ca
> ;
> nstlist  = 12
> nstype   = grid
> pbc  = xyz
> nstcomm  = 100
> rlist= 1.2
> ;
> coulombtype  = PME
> rcoulomb = 1.2
> vdwtype  = shift
> rvdw = 1.2
> ;
> pme_order= 4
> ewald_rtol   = 1e-05
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = no
> fourier_nx   = 32
> fourier_ny   = 32
> fourier_nz   = 32
> ;
> constraints  = hbonds
> lincs_iter   = 4
> ;
> Tcoupl   = nose-hoover
> tc_grps  = System
> ref_t= 400.0
> tau_t= 0.5
> gen_vel  = yes
> gen_temp = 200.0
> gen_seed = 22
> ;
> Pcoupl   = berendsen
> pcoupltype   = anisotropic
> tau_p= 0.5 0.5 0.5 0.5 0.5 0.5
> compressibility  = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
> ref_p= 1.0 1.0 1.0 0.0 0.0 0.0
> 
> 
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Re: [gmx-users] Reg:walls and pbc xy

[vinothkumar mohanakrishnan]

Hi Berk

Thank you. what settings i should change in mdp file (energy minimisation)
to run the energy minimisation for the single liquid-liquid interface
(liquid-vapour interface at the other two extremes) without any issues?
kindly be specific ( what parameter i should change) below is my mdp file.
any help is highly appreciated.

integrator= steep
emtol= 40.0
emstep  = 0.01
nsteps= 1
nstxout= 100
nstvout= 100
nstfout= 100
nstlog= 100
nstenergy= 100
nstlist= 5
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
vdwtype= Cut-off
rvdw= 1.0
ewald_geometry= 3dc
nwall= 2
wall_type= 9-3
wall_r_linpot= 1
wall_atomtype   = opls_966 opls_968
wall_density= 9-3 9-3
wall_ewald_zfac= 3
pbc= xy
fourierspacing  = 0.18

Regards
Vinoth

On Tue, Nov 2, 2010 at 3:41 PM, Berk Hess  wrote:

>  I meant to say that if you see effects of one interface on another with a
> layer of 1 nm thickness/height,
> these effects will be less with a layer of 2 nm thickness and even less
> with 10 nm thickness.
>
> Berk
>
> --
> Date: Tue, 2 Nov 2010 15:30:34 +0530
>
> Subject: Re: [gmx-users] Reg:walls and pbc xy
> From: kmvin...@gmail.com
> To: gmx-users@gromacs.org
>
> Hi Berk
>
> Thank you once again. How can i use thick layers and what is the procedure?
> can you explain it bit more on this?
>
> Regards
> Vinoth
>
> On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess  wrote:
>
>  Hi,
>
> I have not heard about such issues, but it might depend a lot on your
> particular application.
> I would think you will always have disturbances, no matter if you use two
> interfaces,
> one interface with walls or one liquid-liquid interface and two
> liquid-vapour interfaces.
> The only solution to such problems is using thicker layers.
>
> The wall are on the bottom (z=0) and top (z=z_box) of the box, as the
> manual says.
>
> Berk
>
> --
> Date: Tue, 2 Nov 2010 14:59:31 +0530
> Subject: Re: [gmx-users] Reg:walls and pbc xy
>
> From: kmvin...@gmail.com
> To: gmx-users@gromacs.org
>
> Hi Berk
>
> I need only one interface because if i have two interfaces the "capillary
> waves from one interface disturb the other even though the distance between
> the average positions of the two interfaces are larger than the potential
> cut-off" (this was said in the literature).
>
> Can anyone explain me why walls are used for interfaces? and what is the
> purpose of using walls?.
> suppose if i put nwall =2 where exactly are the walls created? can anyone
> explain me with an example?
>
> i read the manual but it is not making any sense to me. if i know this i
> know what correction i should make in my mdp file to make it work for pbc
> xy. any help is highly appreciated.
>
> Regards
> Vinoth
>
> On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess  wrote:
>
>  Hi,
>
> With wall_r_linpot your wall potential is linear from 1 nm downwards.
> Since the LJ force is negative at 1 nm, your atoms are attracted to the
> walls.
>
> But why not simply use two interfaces? You get double the sampling for free
> and you do not have to bother with complicated wall setups.
>
> Berk
>
> --
> Date: Tue, 2 Nov 2010 11:49:48 +0530
> From: kmvin...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Reg:walls and pbc xy
>
>
> Hi Gromacians
>
> I want to create a liquid-liquid interface and study its properties. Hence
> i combined two boxes ( say water and DCE). The two boxes  are well
> equilibrated before merging and i created an interface. Now i want to
> perform energy minimisation for the interface by appling pbc in the xy
> direction and using walls. ( If i apply pbc in all the directions i get two
> interfaces where as i need only one interface hence i am applying it only on
> the xy direction and removing the boundary condition in the Z
> direction.).When i performed the energy minimisation for the interfacial
> system but i found that my system is exploding (several PDB files are
> written while running mdrun is executed) and i dont know why?.There is no
> issue when i use pbc in all directions. below is my em.mdp file. any help is
> highly appreciated.
>
> integrator= steep
> emtol= 40.0
> emstep  = 0.01
> nsteps= 1
> nstxout= 100
> nstvout= 100
> nstfout= 100
> nstlog= 100
> nstenergy= 100
> nstlist= 5
> ns_type= grid
> rlist= 1.0
> coulombtype= PME
> rcoulomb= 1.0
> vdwtype= Cut-off
> rvdw= 1.0
> ewald_geometry= 3dc
> nwall= 2
> wall_type= 9-3
> wall_r_linpot= 1
> wall_atomtype   = opls_966 opls_968
> wall_density= 9-3 9-3
> wall_ewald_zfac= 3
> pbc= xy
> fourierspacing  = 0.18
>
>
> Regards
> Vinoth
>
> -- gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-u

[gmx-users] Re:Re: gmx-users Digest, Vol 79, Issue 8

[Amin Arabbagheri]

Hi Mark,

Are there differences between functions 9 and 1? So can I implement these 
dihedrals in successive lines, just using function 9 or 1?

Amin
--- On Tue, 2/11/10, gmx-users-requ...@gromacs.org 
 wrote:

From: gmx-users-requ...@gromacs.org 
Subject: gmx-users Digest, Vol 79, Issue 8
To: gmx-users@gromacs.org
Date: Tuesday, 2 November, 2010, 5:29

Send gmx-users mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


Today's Topics:

   1. Re: multiple torsions for one dihedral (Mark Abraham)
   2. questions about umbrella sampling (mirc...@sjtu.edu.cn)
   3. RE: Reg:walls and pbc xy (Berk Hess)
   4. Re: Reg:walls and pbc xy (vinothkumar mohanakrishnan)


--

Message: 1
Date: Tue, 02 Nov 2010 17:21:29 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] multiple torsions for one dihedral
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"

Yes, multiple "type 1" dihedrals for use with AMBER and CHARMM forcefields can 
be implemented, either as successive [dihedraltypes] of type 9 (since GROMACS 
4.0, IIRC) or as multiple [dihedrals] of type 1 (since ages).

Mark

- Original Message -
From: Amin Arabbagheri 
Date: Tuesday, November 2, 2010 17:06
Subject: [gmx-users] multiple torsions for one dihedral
To: gmx-users@gromacs.org

---
| > Hi all,
> 
> I'm using AMBER99p force field in GROMACS. In the AMBER forcefield for some 
> dihedrals, there are several values, in which n values are different.  
> As an example, for C3-C3-N-C, I have
> C3-C3-N-C   .50  180.0  -4
> C3-C3-N-C   .15  180.0  -3
> C3-C3-N-C   .53      0.0   1
> 
> For the version 4, is there a convenient way to use these multiple  dihedrals?
> Thanks,
> Amin
> 
 |
---
> 
          > -- 
> gmx-users mailing list    gmx-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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Message: 2
Date: Tue, 02 Nov 2010 15:16:55 +0800
From: mirc...@sjtu.edu.cn
Subject: [gmx-users] questions about umbrella sampling
To: gmx-users@gromacs.org
Message-ID: <20101102151655.msoayn0bno4gk...@webmail.sjtu.edu.cn>
Content-Type: text/plain;    charset=GB2312;    DelSp="Yes";    format="flowed"

Dear All:

I am using umbrella sampling method to calculate potential of mean
force and I encountered the following questions:
1, at the *.ppa file, I need to incorporate a parameter indicating the
"the position of the pull group will restraint to, relative to the
reference group" (i.e., the "pos1" parameter).

To my understanding, in the initial structure, the pull group is not
need to at the exact position defined by the aformationed parameter
("pos1" parameter) in the .ppa file. I just need to put the pull group
near that position, am I right?

2, Since I need to define the position of the pull group relative to
the reference group. I need to calculate the mass center of the
reference group as well as that of the pull group. Does there any
tools in GROMACS to calculate their mass center?

Thank you very much for your time and your kindness!

Best Regards

R-X Gu



- 完成转寄邮件 -




--

Message: 3
Date: Tue, 2 Nov 2010 09:07:19 +0100
From: Berk Hess 
Subject: RE: [gmx-users] Reg:walls and pbc xy
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"


Hi,

With wall_r_linpot your wall potential is linear from 1 nm downwards.
Since the LJ force is negative at 1 nm, your atoms are attracted to the walls.

But why not simply use two interfaces? You get double the sampling for free
and you do not have to bother with complicated wall setups.

Berk

Date: Tue, 2 Nov 2010 11:49:48 +0530
From: kmvin...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Reg:walls and pbc xy

[gmx-users] Re: Charmm36 FF and membrane

[Thomas Piggot]

As I said please keep all correspondence on the GROMACS mailing list for 
general GROMACS problems.


You can use genconf to increase the size of the membrane.

Cheers

Tom

tusar ban wrote:
Thanks for your reply. The link that you have suggested contains the 
POPE structure. However that is too small (by XY dimension) for my 
purpose. I am still trying with Charmm36 FF.

Regards

On Mon, Nov 1, 2010 at 4:21 PM, Thomas Piggot > wrote:


Hi,

This is more of a GROMACS problem than a specific problem related to
this lipid conversion so it is best to keep these questions on the
GROMACS mailing list (I have copied my reply there).

The warning is fairly explanatory, your input POPE structure (for
POPE 315) is missing this hydrogen. This means that whatever you did
in VMD to generate the structure did not add this hydrogen. You
should have been able to solve this by adding the appropriate lines
into the .hdb (which is left empty as the user is expected to
provide an all-atom lipid input structure, the same as in the
CHARMM27 forcefield in GROMACS). I cannot tell why this has not
worked without you providing more details of what you did.

However, rather than trying to either fix what you did in VMD or add
entries into the .hdb, the easiest solution is to your problem is to
just use an available CHARMM36 bilayer as input for pdb2gmx:

http://terpconnect.umd.edu/~jbklauda/research/download.html


Cheers

Tom

tusar ban wrote:

Dear Prof.Piggot,
I am trying to equilibrate POPE membrane (generated though VMD)
using Gromacs 4.5.1 and Charmm36 FF. I have downloaded
"charmm36.ff.tgz
"
from
http://www.gromacs.org/Downloads/User_contributions/Force_fields.
When I do pdb2gmx, I get several warnings, all about H-atoms.
One such typical warning is


"WARNING: atom H6Y is missing in residue POPE 315 in the pdb file
You might need to add atom H6Y to the hydrogen database
of building block POPE
in the file lipids.hdb"

I opened the "lipids.hdb" file and found that is empty. What
could be the reason for this. Is it intentionally kept empty?

When I manually prepare the "lipids.hdb" (following the Gromacs
Manual), I could successfully pdb2gmx, energy minimize the POPE
membrane. However, I could not equilibrate the minimized
structure. During equilibration, mdrun works up to few thousand
steps and then started complaining about LJ 1-4 interactions and
it crashes. I do not know where I went wrong. Please enlighten me.

Best regards.

-- 
Dr. Tusar Bandyopadhyay

Theoretical Chemistry Section,
Chemistry Group
BARC, Trombay
Mumbai 400 085
INDIA
Tel: 022-2559 0300
email: tusaratb...@gmail.com 
>


-- 
Dr Thomas Piggot

University of Southampton, UK.




--
Dr. Tusar Bandyopadhyay
Theoretical Chemistry Section,
Chemistry Group
BARC, Trombay
Mumbai 400 085
INDIA
Tel: 022-2559 0300
email: tusaratb...@gmail.com 



--
Dr Thomas Piggot
University of Southampton, UK.
--
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RE: [gmx-users] Reg:walls and pbc xy

[Berk Hess]

I meant to say that if you see effects of one interface on another with a layer 
of 1 nm thickness/height,
these effects will be less with a layer of 2 nm thickness and even less with 10 
nm thickness.

Berk

Date: Tue, 2 Nov 2010 15:30:34 +0530
Subject: Re: [gmx-users] Reg:walls and pbc xy
From: kmvin...@gmail.com
To: gmx-users@gromacs.org

Hi Berk

Thank you once again. How can i use thick layers and what is the procedure? can 
you explain it bit more on this?

Regards
Vinoth

On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess  wrote:






Hi,

I have not heard about such issues, but it might depend a lot on your 
particular application.
I would think you will always have disturbances, no matter if you use two 
interfaces,
one interface with walls or one liquid-liquid interface and two liquid-vapour 
interfaces.

The only solution to such problems is using thicker layers.

The wall are on the bottom (z=0) and top (z=z_box) of the box, as the manual 
says.

Berk

Date: Tue, 2 Nov 2010 14:59:31 +0530
Subject: Re: [gmx-users] Reg:walls and pbc xy

From: kmvin...@gmail.com
To: gmx-users@gromacs.org

Hi Berk


I need only one interface because if i have two interfaces the "capillary waves 
from one interface disturb the other even though the distance between the 
average positions of the two interfaces are larger than the potential cut-off" 
(this was said in the literature).



Can anyone explain me why walls are used for interfaces? and what is the 
purpose of using walls?. 
suppose if i put nwall =2 where exactly are the walls created? can anyone 
explain me with an example?

i read the manual but it is not making any sense to me. if i know this i know 
what correction i should make in my mdp file to make it work for pbc xy. any 
help is highly appreciated.



Regards
Vinoth

On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess  wrote:







Hi,

With wall_r_linpot your wall potential is linear from 1 nm downwards.
Since the LJ force is negative at 1 nm, your atoms are attracted to the walls.

But why not simply use two interfaces? You get double the sampling for free


and you do not have to bother with complicated wall setups.

Berk

Date: Tue, 2 Nov 2010 11:49:48 +0530
From: kmvin...@gmail.com
To: gmx-users@gromacs.org


Subject: [gmx-users] Reg:walls and pbc xy

Hi Gromacians

I want to create a liquid-liquid interface and study its properties. Hence i 
combined two boxes ( say water and DCE). The two boxes  are well equilibrated 
before merging and i created an interface. Now i want to perform energy 
minimisation for the interface by appling pbc in the xy direction and using 
walls. ( If i apply pbc in all the directions i get two interfaces where as i 
need only one interface hence i am applying it only on the xy direction and 
removing the boundary condition in the Z direction.).When i performed the 
energy minimisation for the interfacial system but i found that my system is 
exploding (several PDB files are written while running mdrun is executed) and i 
dont know why?.There is no issue when i use pbc in all directions. below is my 
em.mdp file. any help is highly appreciated.




integrator= steep
emtol= 40.0  
emstep  = 0.01
nsteps= 1   
nstxout= 100
nstvout= 100  
nstfout= 100
nstlog= 100  



nstenergy= 100  
nstlist= 5
ns_type= grid   
rlist= 1.0
coulombtype= PME 
rcoulomb= 1.0  
vdwtype= Cut-off  
rvdw= 1.0 



ewald_geometry= 3dc
nwall= 2
wall_type= 9-3
wall_r_linpot= 1
wall_atomtype   = opls_966 opls_968
wall_density= 9-3 9-3
wall_ewald_zfac= 3
pbc= xy 
fourierspacing  = 0.18  





Regards
Vinoth


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Re: [gmx-users] Reg:walls and pbc xy

[vinothkumar mohanakrishnan]

Hi Berk

Thank you once again. How can i use thick layers and what is the procedure?
can you explain it bit more on this?

Regards
Vinoth

On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess  wrote:

>  Hi,
>
> I have not heard about such issues, but it might depend a lot on your
> particular application.
> I would think you will always have disturbances, no matter if you use two
> interfaces,
> one interface with walls or one liquid-liquid interface and two
> liquid-vapour interfaces.
> The only solution to such problems is using thicker layers.
>
> The wall are on the bottom (z=0) and top (z=z_box) of the box, as the
> manual says.
>
> Berk
>
> --
> Date: Tue, 2 Nov 2010 14:59:31 +0530
> Subject: Re: [gmx-users] Reg:walls and pbc xy
>
> From: kmvin...@gmail.com
> To: gmx-users@gromacs.org
>
> Hi Berk
>
> I need only one interface because if i have two interfaces the "capillary
> waves from one interface disturb the other even though the distance between
> the average positions of the two interfaces are larger than the potential
> cut-off" (this was said in the literature).
>
> Can anyone explain me why walls are used for interfaces? and what is the
> purpose of using walls?.
> suppose if i put nwall =2 where exactly are the walls created? can anyone
> explain me with an example?
>
> i read the manual but it is not making any sense to me. if i know this i
> know what correction i should make in my mdp file to make it work for pbc
> xy. any help is highly appreciated.
>
> Regards
> Vinoth
>
> On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess  wrote:
>
>  Hi,
>
> With wall_r_linpot your wall potential is linear from 1 nm downwards.
> Since the LJ force is negative at 1 nm, your atoms are attracted to the
> walls.
>
> But why not simply use two interfaces? You get double the sampling for free
> and you do not have to bother with complicated wall setups.
>
> Berk
>
> --
> Date: Tue, 2 Nov 2010 11:49:48 +0530
> From: kmvin...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Reg:walls and pbc xy
>
>
> Hi Gromacians
>
> I want to create a liquid-liquid interface and study its properties. Hence
> i combined two boxes ( say water and DCE). The two boxes  are well
> equilibrated before merging and i created an interface. Now i want to
> perform energy minimisation for the interface by appling pbc in the xy
> direction and using walls. ( If i apply pbc in all the directions i get two
> interfaces where as i need only one interface hence i am applying it only on
> the xy direction and removing the boundary condition in the Z
> direction.).When i performed the energy minimisation for the interfacial
> system but i found that my system is exploding (several PDB files are
> written while running mdrun is executed) and i dont know why?.There is no
> issue when i use pbc in all directions. below is my em.mdp file. any help is
> highly appreciated.
>
> integrator= steep
> emtol= 40.0
> emstep  = 0.01
> nsteps= 1
> nstxout= 100
> nstvout= 100
> nstfout= 100
> nstlog= 100
> nstenergy= 100
> nstlist= 5
> ns_type= grid
> rlist= 1.0
> coulombtype= PME
> rcoulomb= 1.0
> vdwtype= Cut-off
> rvdw= 1.0
> ewald_geometry= 3dc
> nwall= 2
> wall_type= 9-3
> wall_r_linpot= 1
> wall_atomtype   = opls_966 opls_968
> wall_density= 9-3 9-3
> wall_ewald_zfac= 3
> pbc= xy
> fourierspacing  = 0.18
>
>
> Regards
> Vinoth
>
> -- gmx-users mailing list gmx-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
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> -- gmx-users mailing list gmx-users@gromacs.org
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>
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> Please don't post (un)subscribe requests to the

RE: [gmx-users] Reg:walls and pbc xy

[Berk Hess]

Hi,

I have not heard about such issues, but it might depend a lot on your 
particular application.
I would think you will always have disturbances, no matter if you use two 
interfaces,
one interface with walls or one liquid-liquid interface and two liquid-vapour 
interfaces.
The only solution to such problems is using thicker layers.

The wall are on the bottom (z=0) and top (z=z_box) of the box, as the manual 
says.

Berk

Date: Tue, 2 Nov 2010 14:59:31 +0530
Subject: Re: [gmx-users] Reg:walls and pbc xy
From: kmvin...@gmail.com
To: gmx-users@gromacs.org

Hi Berk

I need only one interface because if i have two interfaces the "capillary waves 
from one interface disturb the other even though the distance between the 
average positions of the two interfaces are larger than the potential cut-off" 
(this was said in the literature).


Can anyone explain me why walls are used for interfaces? and what is the 
purpose of using walls?. 
suppose if i put nwall =2 where exactly are the walls created? can anyone 
explain me with an example?

i read the manual but it is not making any sense to me. if i know this i know 
what correction i should make in my mdp file to make it work for pbc xy. any 
help is highly appreciated.


Regards
Vinoth

On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess  wrote:






Hi,

With wall_r_linpot your wall potential is linear from 1 nm downwards.
Since the LJ force is negative at 1 nm, your atoms are attracted to the walls.

But why not simply use two interfaces? You get double the sampling for free

and you do not have to bother with complicated wall setups.

Berk

Date: Tue, 2 Nov 2010 11:49:48 +0530
From: kmvin...@gmail.com
To: gmx-users@gromacs.org

Subject: [gmx-users] Reg:walls and pbc xy

Hi Gromacians

I want to create a liquid-liquid interface and study its properties. Hence i 
combined two boxes ( say water and DCE). The two boxes  are well equilibrated 
before merging and i created an interface. Now i want to perform energy 
minimisation for the interface by appling pbc in the xy direction and using 
walls. ( If i apply pbc in all the directions i get two interfaces where as i 
need only one interface hence i am applying it only on the xy direction and 
removing the boundary condition in the Z direction.).When i performed the 
energy minimisation for the interfacial system but i found that my system is 
exploding (several PDB files are written while running mdrun is executed) and i 
dont know why?.There is no issue when i use pbc in all directions. below is my 
em.mdp file. any help is highly appreciated.



integrator= steep
emtol= 40.0  
emstep  = 0.01
nsteps= 1   
nstxout= 100
nstvout= 100  
nstfout= 100
nstlog= 100  


nstenergy= 100  
nstlist= 5
ns_type= grid   
rlist= 1.0
coulombtype= PME 
rcoulomb= 1.0  
vdwtype= Cut-off  
rvdw= 1.0 


ewald_geometry= 3dc
nwall= 2
wall_type= 9-3
wall_r_linpot= 1
wall_atomtype   = opls_966 opls_968
wall_density= 9-3 9-3
wall_ewald_zfac= 3
pbc= xy 
fourierspacing  = 0.18  




Regards
Vinoth


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[gmx-users] g_energy problem with 4.5.1 and 4.5.2

[Michael Brunsteiner]

Hi everybody,

I run NPT simulations (with the double precision version of mdrun) of a 
polymer melt

with anisotropic pressure scaling The simulation seems to go fine, and the
trajectories look reasonable, but there's something wrong with my 
g_energy output.


=== With 4.5.1 I get weird values for the box dimensions.
The g_energy output gives me something like:

Box-XX  4.7
Box-YX  0.2
Box-YY  5.5
Box-ZX  0.0
Box-ZY  0.0
Box-ZZ  0.0

Mind you This is NOT because the box shrinks so much as both the input and
output structures are roughly cubic with about 5 nm side-length, also if 
these
values were true at least one box length would be shorter than the 
cut-off and
I'd get a fatal error (which i don't). That is the values reported by 
g_energy are

wrong.
For the same system with isotropic pressure scaling there's no problem.

=== If I use g_energy and mdrun versions 4.5.2 then g_energy stops working
altogether, I get:

prompt> g_energy_d -f ener.edr -o test.xvg -s topol.tpr

"Fatal error:
edr file with negative step number or unreasonable time (and without 
version number).
If you want to use the correct frames before the corrupted frame and 
avoid this fatal error set the env.var. GMX_ENX_NO_FATAL"


I tried both:
prompt> export GMX_ENX_NO_FATAL=1
or
prompt> export GMX_ENX_NO_FATAL=1

in both cases I just get:

"File input/output error:
Cannot read energy file header. Corrupt file?"

This I get with g_energy 4.5.2 for output from both mdrun 4.5.1 AND 4.5.2.

mdp file and sys info included below.

thanks for any feedback!

Michael

==

My system:

Linux 2.6.32-5-amd64,
gcc 4.4.5
GNU C Library (Debian EGLIBC 2.11.2-6+squeeze1) stable release version 
2.11.2

CPU: Intel(R) Core(TM) i7 CPU 960 @ 3.20GHz


the mdp file:

integrator   = md
nsteps   = 25
dt   = 0.002
;
nstxtcout= 0
nstenergy= 108
nst_log  = 100
nstxout  = 250
nstvout  = 0
energygrps   = ste ca
;
nstlist  = 12
nstype   = grid
pbc  = xyz
nstcomm  = 100
rlist= 1.2
;
coulombtype  = PME
rcoulomb = 1.2
vdwtype  = shift
rvdw = 1.2
;
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no
fourier_nx   = 32
fourier_ny   = 32
fourier_nz   = 32
;
constraints  = hbonds
lincs_iter   = 4
;
Tcoupl   = nose-hoover
tc_grps  = System
ref_t= 400.0
tau_t= 0.5
gen_vel  = yes
gen_temp = 200.0
gen_seed = 22
;
Pcoupl   = berendsen
pcoupltype   = anisotropic
tau_p= 0.5 0.5 0.5 0.5 0.5 0.5
compressibility  = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
ref_p= 1.0 1.0 1.0 0.0 0.0 0.0


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Re: [gmx-users] Reg:walls and pbc xy

[vinothkumar mohanakrishnan]

Hi Berk

I need only one interface because if i have two interfaces the "capillary
waves from one interface disturb the other even though the distance between
the average positions of the two interfaces are larger than the potential
cut-off" (this was said in the literature).

Can anyone explain me why walls are used for interfaces? and what is the
purpose of using walls?.
suppose if i put nwall =2 where exactly are the walls created? can anyone
explain me with an example?

i read the manual but it is not making any sense to me. if i know this i
know what correction i should make in my mdp file to make it work for pbc
xy. any help is highly appreciated.

Regards
Vinoth

On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess  wrote:

>  Hi,
>
> With wall_r_linpot your wall potential is linear from 1 nm downwards.
> Since the LJ force is negative at 1 nm, your atoms are attracted to the
> walls.
>
> But why not simply use two interfaces? You get double the sampling for free
> and you do not have to bother with complicated wall setups.
>
> Berk
>
> --
> Date: Tue, 2 Nov 2010 11:49:48 +0530
> From: kmvin...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Reg:walls and pbc xy
>
>
> Hi Gromacians
>
> I want to create a liquid-liquid interface and study its properties. Hence
> i combined two boxes ( say water and DCE). The two boxes  are well
> equilibrated before merging and i created an interface. Now i want to
> perform energy minimisation for the interface by appling pbc in the xy
> direction and using walls. ( If i apply pbc in all the directions i get two
> interfaces where as i need only one interface hence i am applying it only on
> the xy direction and removing the boundary condition in the Z
> direction.).When i performed the energy minimisation for the interfacial
> system but i found that my system is exploding (several PDB files are
> written while running mdrun is executed) and i dont know why?.There is no
> issue when i use pbc in all directions. below is my em.mdp file. any help is
> highly appreciated.
>
> integrator= steep
> emtol= 40.0
> emstep  = 0.01
> nsteps= 1
> nstxout= 100
> nstvout= 100
> nstfout= 100
> nstlog= 100
> nstenergy= 100
> nstlist= 5
> ns_type= grid
> rlist= 1.0
> coulombtype= PME
> rcoulomb= 1.0
> vdwtype= Cut-off
> rvdw= 1.0
> ewald_geometry= 3dc
> nwall= 2
> wall_type= 9-3
> wall_r_linpot= 1
> wall_atomtype   = opls_966 opls_968
> wall_density= 9-3 9-3
> wall_ewald_zfac= 3
> pbc= xy
> fourierspacing  = 0.18
>
>
> Regards
> Vinoth
>
> -- gmx-users mailing list gmx-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
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RE: [gmx-users] Reg:walls and pbc xy

[Berk Hess]

Hi,

With wall_r_linpot your wall potential is linear from 1 nm downwards.
Since the LJ force is negative at 1 nm, your atoms are attracted to the walls.

But why not simply use two interfaces? You get double the sampling for free
and you do not have to bother with complicated wall setups.

Berk

Date: Tue, 2 Nov 2010 11:49:48 +0530
From: kmvin...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Reg:walls and pbc xy

Hi Gromacians

I want to create a liquid-liquid interface and study its properties. Hence i 
combined two boxes ( say water and DCE). The two boxes  are well equilibrated 
before merging and i created an interface. Now i want to perform energy 
minimisation for the interface by appling pbc in the xy direction and using 
walls. ( If i apply pbc in all the directions i get two interfaces where as i 
need only one interface hence i am applying it only on the xy direction and 
removing the boundary condition in the Z direction.).When i performed the 
energy minimisation for the interfacial system but i found that my system is 
exploding (several PDB files are written while running mdrun is executed) and i 
dont know why?.There is no issue when i use pbc in all directions. below is my 
em.mdp file. any help is highly appreciated.


integrator= steep
emtol= 40.0  
emstep  = 0.01
nsteps= 1   
nstxout= 100
nstvout= 100  
nstfout= 100
nstlog= 100  

nstenergy= 100  
nstlist= 5
ns_type= grid   
rlist= 1.0
coulombtype= PME 
rcoulomb= 1.0  
vdwtype= Cut-off  
rvdw= 1.0 

ewald_geometry= 3dc
nwall= 2
wall_type= 9-3
wall_r_linpot= 1
wall_atomtype   = opls_966 opls_968
wall_density= 9-3 9-3
wall_ewald_zfac= 3
pbc= xy 
fourierspacing  = 0.18  



Regards
Vinoth


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[gmx-users] questions about umbrella sampling

[mircial]

Dear All:

I am using umbrella sampling method to calculate potential of mean
force and I encountered the following questions:
1, at the *.ppa file, I need to incorporate a parameter indicating the
"the position of the pull group will restraint to, relative to the
reference group" (i.e., the "pos1" parameter).

To my understanding, in the initial structure, the pull group is not
need to at the exact position defined by the aformationed parameter
("pos1" parameter) in the .ppa file. I just need to put the pull group
near that position, am I right?

2, Since I need to define the position of the pull group relative to
the reference group. I need to calculate the mass center of the
reference group as well as that of the pull group. Does there any
tools in GROMACS to calculate their mass center?

Thank you very much for your time and your kindness!

Best Regards

R-X Gu



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