RE: [gmx-users] NVT equilibration of Ethanol in OPLSAA.

[Dallas Warren]

Sounds very much like you have an insufficient number of molecules in the box 
to fill it up.  If you look at the pressure data for the simulation, I suspect 
you will find that it is negative, the box wants to decrease in volume.

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.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Ravi Kumar Venkatraman
Sent: Tuesday, 4 October 2011 6:17 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] NVT equilibration of Ethanol in OPLSAA.

Dear all,
 I have been trying to generate pre-equilibrated ethanol solvent 
box of 512 molecules in OPLSAA ff. I used ethanol.itp in oplsaa.ff directory 
for generating the topology file for ethanol. After NVT equilibration some of 
the molecules get aggregated and there is some void in the box. I tried running 
at faster time scales like 0.2 fs then also I was getting the same. Please help 
me to overcome this problem.

With regards,
Ravi Kumar Venkatraman,
IPC Dept.,
IISc, Bangalore,
INDIA.
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Re: [gmx-users] Getting an .edr file from trajectory

[SebastianWaltz]

On 10/04/2011 09:48 PM, Taylor Kaplan wrote:
> Hi Gromac Users,
>
>   I stupidly overwritten my .edr file, but my .traj file is still intact. Is 
> it possible to use my traj file to recover my energy file. I also have my tpr 
> file which is also in one piece. 
>
>
> Thanks,
>
> Taylor
>
Hi Taylor,

you can use the rerun option of mdrun, if you have stored the full
trajectory including the solvent coordinates.

Sebastian
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[gmx-users] Getting an .edr file from trajectory

[Taylor Kaplan]

Hi Gromac Users,

  I stupidly overwritten my .edr file, but my .traj file is still intact. Is it 
possible to use my traj file to recover my energy file. I also have my tpr file 
which is also in one piece. 


Thanks,

Taylor
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[gmx-users] DNA dangling bond

[Nuria Alegret]

I'm using gromacs version 4.0.5. My system is a double stranded DNA (9 
nucleotides), a bit modified (the DC3 terminal is replaced by another 
one named C5l). When I try to convert the pdb file to a .gro one, a 
message error appear, as follows:

/
Fatal error:
There is a dangling bond at at least one of the terminal ends and the 
force field does not provide terminal entriesor files. Edit a 
.n.tdb and/or .c.tdb file.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors/

Can someone please help?? I was not able to find a solution Thanks 
in advance!!


I attach the pdb file.

Nuria Alegret
University Rovira i Virgili (Spain)
REMARKGENERATED BY TRJCONV
TITLE ICE-DNA in water t= 144.5
REMARKTHIS IS A SIMULATION BOX
CRYST1   45.510   47.780   46.270  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  C4' C5l 1  23.660   9.290  32.750  1.00  0.00
ATOM  2  H4' C5l 1  23.740   8.440  32.110  1.00  0.00
ATOM  3  O4' C5l 1  24.840  10.130  32.710  1.00  0.00
ATOM  4  C1' C5l 1  24.490  11.380  32.210  1.00  0.00
ATOM  5  H1' C5l 1  24.500  12.080  32.970  1.00  0.00
ATOM  6  N1  C5l 1  25.590  11.680  31.220  1.00  0.00
ATOM  7  C6  C5l 1  25.760  11.000  30.060  1.00  0.00
ATOM  8  H6  C5l 1  25.150  10.140  29.960  1.00  0.00
ATOM  9  C5  C5l 1  26.710  11.390  29.170  1.00  0.00
ATOM 10  H5  C5l 1  26.900  10.790  28.250  1.00  0.00
ATOM 11  C4  C5l 1  27.450  12.510  29.500  1.00  0.00
ATOM 12  N4  C5l 1  28.440  13.030  28.750  1.00  0.00
ATOM 13  H41 C5l 1  29.020  13.750  29.140  1.00  0.00
ATOM 14  H42 C5l 1  28.640  12.760  27.820  1.00  0.00
ATOM 15  N3  C5l 1  27.320  13.140  30.660  1.00  0.00
ATOM 16  C2  C5l 1  26.390  12.720  31.520  1.00  0.00
ATOM 17  O   C5l 1  26.370  13.340  32.600  1.00  0.00
ATOM 18  C3' C5l 1  22.480  10.210  32.470  1.00  0.00
ATOM 19  H3' C5l 1  21.710   9.690  31.850  1.00  0.00
ATOM 20  C2' C5l 1  23.100  11.330  31.590  1.00  0.00
ATOM 21 1H2' C5l 1  23.000  11.000  30.540  1.00  0.00
ATOM 22 2H2' C5l 1  22.500  12.220  31.630  1.00  0.00
ATOM 23  O3' C5l 1  21.910  10.520  33.690  1.00  0.00
ATOM 24  P   DG0 2  20.580  11.420  33.810  1.00  0.00
ATOM 25  O1P DG0 2  20.020  11.250  35.090  1.00  0.00
ATOM 26  O2P DG0 2  19.750  11.410  32.640  1.00  0.00
ATOM 27  O5' DG0 2  21.140  12.920  33.820  1.00  0.00
ATOM 28  C5' DG0 2  22.030  13.280  34.910  1.00  0.00
ATOM 29 1H5' DG0 2  21.640  13.100  35.870  1.00  0.00
ATOM 30 2H5' DG0 2  22.960  12.740  34.820  1.00  0.00
ATOM 31  C4' DG0 2  22.440  14.750  34.680  1.00  0.00
ATOM 32  H4' DG0 2  22.930  15.190  35.570  1.00  0.00
ATOM 33  O4' DG0 2  23.490  14.760  33.790  1.00  0.00
ATOM 34  C1' DG0 2  23.290  15.860  32.850  1.00  0.00
ATOM 35  H1' DG0 2  23.750  16.790  33.330  1.00  0.00
ATOM 36  N9  DG0 2  23.770  15.550  31.540  1.00  0.00
ATOM 37  C8  DG0 2  23.270  14.620  30.660  1.00  0.00
ATOM 38  H8  DG0 2  22.330  14.130  30.910  1.00  0.00
ATOM 39  N7  DG0 2  23.840  14.510  29.530  1.00  0.00
ATOM 40  C5  DG0 2  24.950  15.320  29.750  1.00  0.00
ATOM 41  C6  DG0 2  26.110  15.600  28.900  1.00  0.00
ATOM 42  O6  DG0 2  26.400  15.280  27.700  1.00  0.00
ATOM 43  N1  DG0 2  26.970  16.540  29.380  1.00  0.00
ATOM 44  H1  DG0 2  27.820  16.700  28.850  1.00  0.00
ATOM 45  C2  DG0 2  26.770  17.140  30.590  1.00  0.00
ATOM 46  N2  DG0 2  27.630  18.090  30.820  1.00  0.00
ATOM 47  H21 DG0 2  28.540  18.110  30.320  1.00  0.00
ATOM 48  H22 DG0 2  27.460  18.480  31.700  1.00  0.00
ATOM 49  N3  DG0 2  25.810  16.860  31.460  1.00  0.00
ATOM 50  C4  DG0 2  24.990  15.890  30.980  1.00  0.00
ATOM 51  C3' DG0 2  21.280  15.710  34.260  1.00  0.00
ATOM 52  H3' DG0 2  20.270  15.300  34.2

Re: [gmx-users] RMSD bonds and angles

[Tsjerk Wassenaar]

Hey :)

If that is what you want, you'll have to turn to programming. But what do
you think to gain from it? First get to the bottom of things you can do with
gromacs already. Then, if the tools available don't help in answering your
question, think of what you'd need to get it done.

Cheers,

Tsjerk

On Oct 4, 2011 12:06 PM, "ahmet yıldırım"  wrote:


No, it calculates with respect to the positions atom. but I want to
calculate the RMSD bonds (A˚ ) and RMSD angles (o).

2011/10/4 Mark Abraham  > > On 4/10/2011 7:05 PM,
ahmet yıldırım wrote: >...

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Re: [gmx-users] how to install the gromacs-4.5.5 with the gpu on the linux

[Mark Abraham]

On 5/10/2011 2:10 AM, 杜波 wrote:

i see the instructions on the web:

Installing
Download and unpack the binary package for the respective OS and


You are instructed to get a binary package. However, above this text is 
an updated set of instructions that declares the binary packages are 
deprecated. Whoever did the update to this page expected you to read all 
of the text, unfortunately.



architecture. Copy the content of the package to your normal Gromacs
installation directory (or to a custom location). Note that the
distributed Gromacs-GPU packages do not contain the entire set of
tools and utilities included in a full Gromacs installation.
Therefore, it is recommended to have a ≥v4.5 standard Gromacs
installation along the GPU accelerated one.
Add the openmm/lib directory to your library path, e.g. in bash:
export LD_LIBRARY_PATH=path_to_gromacs/openmm/lib:$LD_LIBRARY_PATH
If there are other OpenMM versions installed, make sure that the
supplied libraries have preference when running mdrun-gpu. Also, make
sure that the CUDA libraries installed match the version of CUDA with
which Gromacs-GPU is compiled.
Set the OPENMM_PLUGIN_DIR environment variable to contain the path to
the openmm/lib/plugins directory, e.g. in bash:
export OPENMM_PLUGIN_DIR=path_to_gromacs/openmm/lib/plugins
At this point, running the command path_to_gromacs/bin/mdrun-gpu -h
should display the standard mdrun help which means that the binary
runs and all the necessary libraries are accessible.

and download the gromacs-4.5.5.tar.gz on the http://www.gromacs.org/Downloads,


This is a package of source code. If you read further on the page, there 
are instructions for building from the source code. You will need to 
consult the regular install-from-source instructions also.


Mark

and then unpack it, but i not find the file openmm!
how can i do, if i want to install  gromacs-4.5.5 with the gpu on the
linux ?thanks!

Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com


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[gmx-users] how to install the gromacs-4.5.5 with the gpu on the linux

[杜波]

i see the instructions on the web:

Installing
Download and unpack the binary package for the respective OS and
architecture. Copy the content of the package to your normal Gromacs
installation directory (or to a custom location). Note that the
distributed Gromacs-GPU packages do not contain the entire set of
tools and utilities included in a full Gromacs installation.
Therefore, it is recommended to have a ≥v4.5 standard Gromacs
installation along the GPU accelerated one.
Add the openmm/lib directory to your library path, e.g. in bash:
export LD_LIBRARY_PATH=path_to_gromacs/openmm/lib:$LD_LIBRARY_PATH
If there are other OpenMM versions installed, make sure that the
supplied libraries have preference when running mdrun-gpu. Also, make
sure that the CUDA libraries installed match the version of CUDA with
which Gromacs-GPU is compiled.
Set the OPENMM_PLUGIN_DIR environment variable to contain the path to
the openmm/lib/plugins directory, e.g. in bash:
export OPENMM_PLUGIN_DIR=path_to_gromacs/openmm/lib/plugins
At this point, running the command path_to_gromacs/bin/mdrun-gpu -h
should display the standard mdrun help which means that the binary
runs and all the necessary libraries are accessible.

and download the gromacs-4.5.5.tar.gz on the http://www.gromacs.org/Downloads,
and then unpack it, but i not find the file openmm!
how can i do, if i want to install  gromacs-4.5.5 with the gpu on the
linux ?thanks!

Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com
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Re: [gmx-users] Dihedral transition times for a non-protein structure

[Giulio Tesei]

I'm sorry, actually I forgot to add the flag in the email but I added it
when I started the program.

g_angle -f traj.trr -s topol.tpr -n dihe.ndx -oh histo.xvg -type dihedral
I get the following output:

Group 0 (Phi=0.0_3_5.92) has   232 elements
There is one group in the index
Reading file diheA3.tpr, VERSION 3.3.3 (single precision)
trn version: GMX_trn_file (single precision)
Last frame  1 time 2.000
Found points in the range from 0 to 359 (max 360)
 < angle >  = 0.374572
< angle^2 > = 262.338
Std. Dev.   = 16.1925
Order parameter S^2 = 0.344698

but it generates only a angdist.xvg file.
I'm wondering why it's not generating the histo.xvg file.
Thanks for your help!

2011/10/4 Justin A. Lemkul 

>
>
> Giulio Tesei wrote:
>
>> Hi!
>> I'm performing the analysis of a 30 residues PVA polymer chain in SPC
>> water.
>> I'm trying to find the dihedral transition times of each residue (possibly
>> as an histogram 'number of transitions vs. residue number').
>> I've already tried:
>>
>> 1) g_angle -f traj.trr -s topol.tpr -n angle.ndx -oh histo.xvg
>> but it gives no output besides angdist.xvg
>>
>>
> Add "-type dihedral" to this command, otherwise the analysis is for normal
> angles.
>
> -Justin
>
>
>  2) g_dih -f traj.trr -s topol.tpr -o dihe.out
>> but it gives no output besides an empty dihe.out
>>
>> 3) g_chi (it says there are no dihedral angles in the structure. I guess
>> that this program is for proteins only and it doesn't recognize PVA backbone
>> dihedrals...).
>> I've tried these programs on both gromacs 4.5.3 and gromacs 3.3.3.
>>
>> Thanks for any incoming help!
>>
>> Giulio
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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[gmx-users] quick question about "direction_periodic"

[Natalie Stephenson]

Hi guys,

I was just wondering if with "direction_periodic" the pull simulations pulls at 
both ends of the protein rather than just one.

I've previously been position restraining the C-terminus of my protein and 
pulling on the N-terminus.  With the "distance" pull code this seems to do 
exactly that - hold the C- and pull the N- away from it.  Changing over to the 
"direction_periodic" it seems that the force is being applied to both the C- 
and N- termini even though the position restraint file has been specified when 
creating the .tpr with grompp ... is this right? How can I stop it from pulling 
on both termini if this is in fact the case?

Thanks
Natalie



Natalie Stephenson, B.Sc
PhD Research Associate

Manchester Interdisciplinary Biocentre
131 Princess Street
Manchester
M1 7DN
x65816

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Re: [gmx-users] Dihedral transition times for a non-protein structure

[Justin A. Lemkul]

Giulio Tesei wrote:

Hi!
I'm performing the analysis of a 30 residues PVA polymer chain in SPC 
water.
I'm trying to find the dihedral transition times of each residue 
(possibly as an histogram 'number of transitions vs. residue number').

I've already tried:

1) g_angle -f traj.trr -s topol.tpr -n angle.ndx -oh histo.xvg
but it gives no output besides angdist.xvg



Add "-type dihedral" to this command, otherwise the analysis is for normal 
angles.

-Justin


2) g_dih -f traj.trr -s topol.tpr -o dihe.out
but it gives no output besides an empty dihe.out

3) g_chi (it says there are no dihedral angles in the structure. I guess 
that this program is for proteins only and it doesn't recognize PVA 
backbone dihedrals...).

I've tried these programs on both gromacs 4.5.3 and gromacs 3.3.3.

Thanks for any incoming help!

Giulio



--


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


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[gmx-users] Dihedral transition times for a non-protein structure

[Giulio Tesei]

Hi!
I'm performing the analysis of a 30 residues PVA polymer chain in SPC water.

I'm trying to find the dihedral transition times of each residue (possibly
as an histogram 'number of transitions vs. residue number').
I've already tried:

1) g_angle -f traj.trr -s topol.tpr -n angle.ndx -oh histo.xvg
but it gives no output besides angdist.xvg

2) g_dih -f traj.trr -s topol.tpr -o dihe.out
but it gives no output besides an empty dihe.out

3) g_chi (it says there are no dihedral angles in the structure. I guess
that this program is for proteins only and it doesn't recognize PVA backbone
dihedrals...).
I've tried these programs on both gromacs 4.5.3 and gromacs 3.3.3.

Thanks for any incoming help!

Giulio
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Re: [gmx-users] partial atomic charges

[Justin A. Lemkul]

MARY VARUGHESE wrote:

Hi,
I read the standard advice for parametrization.
But,
Can anyone suggest the ideal force field and QM method( for 
paramterization using gaussian say, HF, DFT etc) to study the 
interaction between a protein and a ligand when i am using GROMCAs 
simulation program.
 


I'd say there is no definitive answer to that question.  Each force field has 
strengths and weaknesses and requires a different type of parameterization.


-Justin


Thanking you
Mary
--- On *Tue, 4/10/11, Mark Abraham //* wrote:


From: Mark Abraham 
Subject: Re: [gmx-users] partial atomic charges
To: "Discussion list for GROMACS users" 
Date: Tuesday, 4 October, 2011, 12:06 PM

On 4/10/2011 5:20 PM, MARY VARUGHESE wrote:

Hi,

I , am working on interaction between proteins/nucleic acids and
ligands.
On deriving partial atomic charges using gaussian can anyone suggest,
among HF-6-31G* and B3LYP-6-31G which one is ideal(or any other
one to suggest) and why?
I mean to get the partial atomic charges of the ligand which i
have to dock to a protein, which charge derivation method is ideal
for gromacs.

Your suggestions will be very much helpful.



The standard advice for parametrization can be found here
http://www.gromacs.org/Documentation/How-tos/Parameterization

Mark

-Inline Attachment Follows-

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--


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


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Re: [gmx-users] RMSD bonds and angles

[ahmet yıldırım]

No, it calculates with respect to the positions atom. but I want to
calculate the RMSD bonds (A˚ ) and RMSD angles (o).

2011/10/4 Mark Abraham 

>  On 4/10/2011 7:05 PM, ahmet yıldırım wrote:
>
> any hints? :(
>
>
> You didn't find something useful in the section titled "Root mean square
> deviations in structure"?
>
> Mark
>
>
> 03 Ekim 2011 22:32 tarihinde ahmet yıldırım  yazdı:
>
>> I look at chapter 8 but I didnt found that I want. can you give a hint?
>> Thanks
>>
>>
>> 2011/10/3 Mark Abraham 
>>
>>> On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
>>>
 Dear users,

 How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?

>>>
>>>  Please start your search in chapter 8 of the manual, and consider doing
>>> some tutorial material. Someone is likely to have covered some similar
>>> procedures.
>>>
>>> Mark
>>>  --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>
>>
>>
>>
>>  --
>> Ahmet YILDIRIM
>>
>
>
>
> --
> Ahmet YILDIRIM
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] partial atomic charges

[MARY VARUGHESE]

Hi,
I read the standard advice for parametrization.
But,
Can anyone suggest the ideal force field and QM method( for paramterization 
using gaussian say, HF, DFT etc) to study the interaction between a protein and 
a ligand when i am using GROMCAs simulation program.
 
Thanking you 
Mary
--- On Tue, 4/10/11, Mark Abraham  wrote:


From: Mark Abraham 
Subject: Re: [gmx-users] partial atomic charges
To: "Discussion list for GROMACS users" 
Date: Tuesday, 4 October, 2011, 12:06 PM


On 4/10/2011 5:20 PM, MARY VARUGHESE wrote: 




Hi,

I , am working on interaction between proteins/nucleic acids and ligands. 
On deriving partial atomic charges using gaussian can anyone suggest,
among HF-6-31G* and B3LYP-6-31G which one is ideal(or any other one to suggest) 
and why?
I mean to get the partial atomic charges of the ligand which i have to dock to 
a protein, which charge derivation method is ideal for gromacs.

Your suggestions will be very much helpful.

The standard advice for parametrization can be found here 
http://www.gromacs.org/Documentation/How-tos/Parameterization

Mark

-Inline Attachment Follows-


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Re: [gmx-users] Creating topology with bonds over pbc

[Mark Abraham]

On 4/10/2011 6:25 PM, Wojciech Müller wrote:

Hi all,
Let's say I created a pdb of a B-DNA Double-Helix with amber tools. 
Now I would like to have a topology in which the last residues are 
bonded to the first. How can I do that expect of actually mess 
together a topology file by self written scripts and/or handwork? 


I've never done anything like it, but I would guess that you can
* generate with AMBER tools an equivalent non-periodic structure with 
suitable termini (you need the ordering of the atoms belonging to 
non-terminal monomers to match the ordering of your structure above),

* use pdb2gmx on that,
* take the top file and remove the atoms for the termini, and the 
intra-termini bonds,

* create the head-to-tail [ bonds ] in the .top file, and
* match that with your structure above for grompp.
Sounds like about 15 minutes' work, if you already know the .top file 
format and how to use AMBER tools.


Mark

Also if create helix strings without substituting the terminal 
phosphate pdb2gmx doesn't seem to accept it.

Thanks for any hints,
W.Müller


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Re: [gmx-users] NVT equilibration of Ethanol in OPLSAA.

[Mark Abraham]

On 4/10/2011 6:16 PM, Ravi Kumar Venkatraman wrote:

*Dear all,
 I have been trying to generate pre-equilibrated ethanol 
solvent box of 512 molecules in **OPLSAA ff. I used ethanol.itp in 
oplsaa.ff directory for generating the topology file for ethanol. 
After NVT equilibration some of the molecules get aggregated and there 
is some void in the box. I tried running at faster time scales like 
0.2 fs then also I was getting the same. Please help me to overcome 
this problem.*


You should follow the suggestions here 
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation. Even 
if you have, we'd need a lot more detailed information about your 
procedure and parameters to be able to guess what might have gone wrong.


Mark
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Re: [gmx-users] RMSD bonds and angles

[Mark Abraham]

On 4/10/2011 7:05 PM, ahmet y?ld?r?m wrote:

any hints? :(


You didn't find something useful in the section titled "Root mean square 
deviations in structure"?


Mark


03 Ekim 2011 22:32 tarihinde ahmet y?ld?r?m > yazd?:


I look at chapter 8 but I didnt found that I want. can you give a
hint?
Thanks


2011/10/3 Mark Abraham mailto:mark.abra...@anu.edu.au>>

On 3/10/2011 10:29 PM, ahmet y?ld?r?m wrote:

Dear users,

How can I calculate the RMSD bonds (A? ) and RMSD angles (o)?


Please start your search in chapter 8 of the manual, and
consider doing some tutorial material. Someone is likely to
have covered some similar procedures.

Mark
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-- 
Ahmet YILDIRIM





--
Ahmet YILDIRIM




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Re: [gmx-users] RMSD bonds and angles

[ahmet yıldırım]

any hints? :(

03 Ekim 2011 22:32 tarihinde ahmet yıldırım  yazdı:

> I look at chapter 8 but I didnt found that I want. can you give a hint?
> Thanks
>
>
> 2011/10/3 Mark Abraham 
>
>> On 3/10/2011 10:29 PM, ahmet yıldırım wrote:
>>
>>> Dear users,
>>>
>>> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)?
>>>
>>
>> Please start your search in chapter 8 of the manual, and consider doing
>> some tutorial material. Someone is likely to have covered some similar
>> procedures.
>>
>> Mark
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  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
>>
>
>
>
> --
> Ahmet YILDIRIM
>



-- 
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[gmx-users] Creating topology with bonds over pbc

[Wojciech Müller]

Hi all,
Let's say I created a pdb of a B-DNA Double-Helix with amber tools. Now 
I would like to have a topology in which the last residues are bonded to 
the first. How can I do that expect of actually mess together a topology 
file by self written scripts and/or handwork? Also if create helix 
strings without substituting the terminal phosphate pdb2gmx doesn't seem 
to accept it.

Thanks for any hints,
W.Müller
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[gmx-users] NVT equilibration of Ethanol in OPLSAA.

[Ravi Kumar Venkatraman]

*Dear all,
 I have been trying to generate pre-equilibrated ethanol solvent
box of 512 molecules in **OPLSAA ff. I used ethanol.itp in oplsaa.ff
directory for generating the topology file for ethanol. After NVT
equilibration some of the molecules get aggregated and there is some void in
the box. I tried running at faster time scales like 0.2 fs then also I was
getting the same. Please help me to overcome this problem.

With regards,
Ravi Kumar Venkatraman,
IPC Dept.,
IISc, Bangalore,
INDIA.*
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