Re: [gmx-users] VDW radii of Br and K+

[David van der Spoel]

On 2010-08-24 22.53, nishap.pa...@utoronto.ca wrote:

Hello,

I converted a .tpr file for Bromine ion and Potassium ion using -mead
option and editconf. It gives out the Van der Waals radius of the atom,
but I don't understand why i got ~2.46A for Potassium and ~2.31A for
Bromide. Isn't the bromide ion bigger than Potassium? And I used genion
to add both the atoms.

This is a force field quirk. From the oplsaa.ff/ffnonbonded.itp

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
opls_402  Br- 35 79.90400-1.000   A4.62376e-01  3.76560e-01
opls_408  K+  19 39.09830 1.000   A4.93463e-01  1.37235e-03

You see that K+ has larger sigma than Br-.




Thanks.

-Nisha P




--
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Dept. of Cell & Molec. Biol., Uppsala University.
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Re: [gmx-users] Lysozyme benchmarking for gromacs-4,0.5

[Mark Abraham]

- Original Message -
From: vivek sharma 
Date: Wednesday, August 25, 2010 16:48
Subject: [gmx-users] Lysozyme benchmarking for gromacs-4,0.5
To: Discussion list for GROMACS users 

> Hi there,
> I am running a GROMACS benchmarking on my cluster with the Lysozyme example 
> provided in benchmarking files. I am looking at ns/day to compare the 
> performance of various runs. 
> I am using gromacs-4.0.5, Can somebody provide me with the figures to compare 
> the performance? Also DO I need to take other parameters than ns/day like 
> PP/PME load imbalance to compare the performance?

The GROMACS 4 paper has some relevant benchmark results.

Mark

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[gmx-users] Lysozyme benchmarking for gromacs-4,0.5

[vivek sharma]

Hi there,
I am running a GROMACS benchmarking on my cluster with the Lysozyme example
provided in benchmarking files. I am looking at ns/day to compare the
performance of various runs.
I am using gromacs-4.0.5, Can somebody provide me with the figures to
compare the performance? Also DO I need to take other parameters than ns/day
like PP/PME load imbalance to compare the performance?
Please comment if anybody have tried such runs.

Thanks,
Vivek
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[gmx-users] about the option pull_dim

[DeChang Li]

Dear all,

 Does the following three options do the same things in the pull code of
Gromacs 4.0:

1.  pull_dim = Y Y Y
 pull_vec1 = 1 0 0

**
2.  pull_dim = Y N N
 pull_vec1 = 1 0 0

**
3.  pull_dim = Y N N
 pull_vec1 = 1 0.5 0.5
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Re: [gmx-users] How to do rdf with out normalization?

[Xiaoling Leng]

Thank  you very much:)

2010/8/24 Justin A. Lemkul 

>
>
> Xiaoling Leng wrote:
>
>> Hi all, I want to compute the Radial distribution function with out
>> normalization, using g_rdf.
>> Or in another word, I want use g_rdf to count the numbers of the times
>> that 2 groups in certain distances. How could I do that? Could I use
>>
>
> You might extract some useful information with g_dist -dist.
>
>
>  some method to change the option -norm in g_rdf which in default is
>> "yes" to "no"?
>>
>>
> The switch would be -nonorm.
>
> -Justin
>
>
>  Thanks in advance.
>>
>> Xiaoling Leng
>>
>
> --
> 
>
> 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] VDW radii of Br and K+

[Mark Abraham]

- Original Message -
From: nishap.pa...@utoronto.ca
Date: Wednesday, August 25, 2010 6:54
Subject: [gmx-users] VDW radii of Br and K+
To: gmx-users@gromacs.org

> Hello,
> 
> I converted a .tpr file for Bromine ion and 
> Potassium ion using -mead option and editconf. It gives out the 
> Van der Waals radius of the atom, but I don't understand why i 
> got ~2.46A for Potassium and ~2.31A for Bromide. Isn't the 
> bromide ion bigger than Potassium? And I used genion to add both 
> the atoms.

When something goes wrong, there has to be a chance that you've done the wrong 
thing. Supplying information like exact command lines and names of force fields 
has to help you get better help.

Mark

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Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

[Alan]

Dear Berk,

I understand your point and this can be very confusing.

I am aware that I could use HIS and then pdb2gmx ... -his (option 1), but
this is not working either with rev. d6298. Error:

[snip]
Which HISTIDINE type do you want for residue 3
0. H on ND1 only (HID)
1. H on NE2 only (HIE)
2. H on ND1 and NE2 (HIP)
3. Coupled to Heme (HIS1)

Type a number:1
Identified residue HIS1 as a starting terminus.
Identified residue HIS3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS1HIS2
   NE214   NE231
HIS2   NE231   0.854
HIS3   NE248   0.751   0.847

---
Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d6298
Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line:
552

Fatal error:
Residue 'HISE' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

The pdb I am using is hhh.pdb
ATOM  1  N   HIS 1   3.389   1.609  -0.001  1.00  0.00
N
ATOM  2  H1  HIS 1   4.107   0.893  -0.048  1.00  0.00
H
ATOM  3  H2  HIS 1   2.795   1.549  -0.816  1.00  0.00
H
ATOM  4  H3  HIS 1   2.844   1.452   0.836  1.00  0.00
H
ATOM  5  CA  HIS 1   4.058   2.928   0.075  1.00  0.00
C
ATOM  6  HA  HIS 1   3.894   3.469  -0.857  1.00  0.00
H
ATOM  7  CB  HIS 1   3.469   3.750   1.230  1.00  0.00
C
ATOM  8  HB2 HIS 1   2.384   3.783   1.126  1.00  0.00
H
ATOM  9  HB3 HIS 1   3.695   3.231   2.164  1.00  0.00
H
ATOM 10  CG  HIS 1   3.956   5.172   1.373  1.00  0.00
C
ATOM 11  ND1 HIS 1   4.013   5.834   2.591  1.00  0.00
N
ATOM 12  CE1 HIS 1   4.604   7.011   2.356  1.00  0.00
C
ATOM 13  HE1 HIS 1   4.832   7.752   3.115  1.00  0.00
H
ATOM 14  NE2 HIS 1   4.919   7.122   1.056  1.00  0.00
N
ATOM 15  HE2 HIS 1   5.505   7.845   0.657  1.00  0.00
H
ATOM 16  CD2 HIS 1   4.479   5.987   0.403  1.00  0.00
C
ATOM 17  HD2 HIS 1   4.620   5.781  -0.645  1.00  0.00
H
ATOM 18  C   HIS 1   5.564   2.693   0.196  1.00  0.00
C
ATOM 19  O   HIS 1   5.947   1.551   0.422  1.00  0.00
O
ATOM 20  N   HIS 2   6.376   3.718  -0.053  1.00  0.00
N
ATOM 21  H   HIS 2   5.980   4.646  -0.135  1.00  0.00
H
ATOM 22  CA  HIS 2   7.843   3.744  -0.109  1.00  0.00
C
ATOM 23  HA  HIS 2   8.260   3.319   0.806  1.00  0.00
H
ATOM 24  CB  HIS 2   8.319   2.925  -1.327  1.00  0.00
C
ATOM 25  HB2 HIS 2   7.855   1.940  -1.312  1.00  0.00
H
ATOM 26  HB3 HIS 2   7.985   3.435  -2.233  1.00  0.00
H
ATOM 27  CG  HIS 2   9.807   2.703  -1.450  1.00  0.00
C
ATOM 28  ND1 HIS 2  10.461   2.463  -2.655  1.00  0.00
N
ATOM 29  CE1 HIS 2  11.770   2.542  -2.382  1.00  0.00
C
ATOM 30  HE1 HIS 2  12.557   2.484  -3.124  1.00  0.00
H
ATOM 31  NE2 HIS 2  11.969   2.794  -1.078  1.00  0.00
N
ATOM 32  HE2 HIS 2  12.817   3.173  -0.672  1.00  0.00
H
ATOM 33  CD2 HIS 2  10.740   2.839  -0.459  1.00  0.00
C
ATOM 34  HD2 HIS 2  10.579   3.098   0.574  1.00  0.00
H
ATOM 35  C   HIS 2   8.279   5.228  -0.214  1.00  0.00
C
ATOM 36  O   HIS 2   7.440   6.079  -0.525  1.00  0.00
O
ATOM 37  N   HIS 3   9.547   5.520   0.075  1.00  0.00
N
ATOM 38  H   HIS 3  10.192   4.759   0.245  1.00  0.00
H
ATOM 39  CA  HIS 3  10.254   6.807   0.049  1.00  0.00
C
ATOM 40  HA  HIS 3  10.021   7.358  -0.860  1.00  0.00
H
ATOM 41  CB  HIS 3   9.841   7.621   1.297  1.00  0.00
C
ATOM 42  HB2 HIS 3   8.754   7.687   1.320  1.00  0.00
H
ATOM 43  HB3 HIS 3  10.158   7.074   2.185  1.00  0.00
H
ATOM 44  CG  HIS 3  10.359   9.037   1.429  1.00  0.00
C
ATOM 45  ND1 HIS 3  10.137   9.848   2.546  1.00  0.00
N
ATOM 46  CE1 HIS 3  10.788  10.994   2.308  1.00  0.00
C
ATOM 47  HE1 HIS 3  10.849  11.818   3.006  1.00  0.00
H
ATOM 48  NE2 HIS 3  11.375  10.962   1.100  1.00  0.00
N
ATOM 49  HE2 HIS 3  11.977  11.674   0.715  1.00  0.00
H
ATOM 50  CD2 HIS 3  11.100   9.742   0.525  1.00  0.00
C
ATOM 51  HD2 HIS 3  11.456   9.376  -0.428  1.00  0.00
H
ATOM 52  C   HIS 3  11.761   6.487   0.002  1.00  0.00
C
ATOM 53  O   HIS 3  12.128   5.407   0.518  1.00  0.00
O
ATOM 54  OXT HIS 3  12.494   7.275  -0.632  1.00  0.00
O

Now, using HIE (HHH.pdb, like hhh.pdb but HIE for res instead of HIS) with
export GMX_FFRTP_TER_RENAME=1 and then

pdb2gmx -f HHH.pdb -o HHH.pdb -p agHHH.top -ff amber99sb -

Re: [gmx-users] How to do rdf with out normalization?

[Justin A. Lemkul]

Xiaoling Leng wrote:

Hi all, I want to compute the Radial distribution function with out
normalization, using g_rdf.
Or in another word, I want use g_rdf to count the numbers of the times
that 2 groups in certain distances. How could I do that? Could I use


You might extract some useful information with g_dist -dist.


some method to change the option -norm in g_rdf which in default is
"yes" to "no"?



The switch would be -nonorm.

-Justin


Thanks in advance.

Xiaoling Leng


--


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] Epsilon AA, Epsilon AB, Epsilon BB

[KS Rotondi]

The link takes me to the Tab Potentials page, but using the latest  
Firefox with Mac OS 10.5.8 there are gaps in the text but no functions  
shown at the top of the page. E.g. generic form is:  several blank  
lines, LJ form is: even more blank lines, etc.




On Aug 24, 2010, at 3:48 PM, Justin A. Lemkul wrote:




Rohit Malshe wrote:
Dear all, I want to use a system in which Epsilon AA = 1 and  
Epsilon BB = 0.5.  But I want to use Epsilon AB = 1.5. How do I do  
that in gromacs?


http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

-Justin

--


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


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Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB

[Justin A. Lemkul]

KS Rotondi wrote:
The link takes me to the Tab Potentials page, but using the latest 
Firefox with Mac OS 10.5.8 there are gaps in the text but no functions 
shown at the top of the page. E.g. generic form is:  several blank 
lines, LJ form is: even more blank lines, etc.




Looks like the LaTeX objects are broken again.  I'll see if I can't get them 
worked out, or otherwise just re-work the page.


-Justin




On Aug 24, 2010, at 3:48 PM, Justin A. Lemkul wrote:




Rohit Malshe wrote:
Dear all, I want to use a system in which Epsilon AA = 1 and Epsilon 
BB = 0.5.  But I want to use Epsilon AB = 1.5. How do I do that in 
gromacs?


http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

-Justin

--


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


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--


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] VDW radii of Br and K+

[nishap . patel]

Hello,

I converted a .tpr file for Bromine ion and Potassium ion using  
-mead option and editconf. It gives out the Van der Waals radius of  
the atom, but I don't understand why i got ~2.46A for Potassium and  
~2.31A for Bromide. Isn't the bromide ion bigger than Potassium? And I  
used genion to add both the atoms.


Thanks.

-Nisha P

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[gmx-users] pbc atom

[chris . neale]

Tsjerk,

Two reasons. First, I simply don't understand awk as well as you do.  
Second, I think that breaking it down into simpler commands linked by  
pipes is better for teaching. If somebody needs help to combine 3 cols  
into a vector distance, then they may copy and paste your solution to  
good effect, but may not learn how to apply that technique to another  
problem as easily as they could when seeing the individual actions  
split by pipes. I could easily be wrong on that, but I'm trying to  
provide an answer to your "why" in case you were asking in earnest.


Aside, thanks again for the awk tips, I appreciate them always and  
they are useful to me.


Chris.


directly. I think you want this (assuming that cols 5,6,7 give you the
dx,dy,dz, which I believe that they do):

cat pullx.xvg | grep -v '[#|@]' | awk '{print $1,sqrt($5*$5+$6*$6+$7*$7)}' >
my.data


Nothing directly harmful of course, but why using three programs for
this? awk will do fine:

awk '/^...@]/{print $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data

Tsjerk

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Re: [gmx-users] pbc atom

[Tsjerk Wassenaar]

Hey,

> directly. I think you want this (assuming that cols 5,6,7 give you the
> dx,dy,dz, which I believe that they do):
>
> cat pullx.xvg | grep -v '[#|@]' | awk '{print $1,sqrt($5*$5+$6*$6+$7*$7)}' >
> my.data

Nothing directly harmful of course, but why using three programs for
this? awk will do fine:

awk '/^...@]/{print $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB

[David van der Spoel]

On 8/24/10 8:38 PM, Rohit Malshe wrote:

Dear all,

I want to use a system in which

Epsilon AA = 1 and Epsilon BB = 0.5.

But I want to use Epsilon AB = 1.5.

How do I do that in gromacs?


You can specify nonbonded parameters per atompair. Check topology 
section in the manual.

[ nonbond_params]
; i j type c6 c12
O O 1  1 1
N N 1 0.5 0.5
O N 1 1.5 1.5

whatever

--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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RE: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB

[Osmair Oliveira]

If you will use Lennard-Jones potential, you can combine both epsilons:
AB = sqrt(AA*BB)

Osmair

> Date: Tue, 24 Aug 2010 15:48:56 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB
> 
> 
> 
> Rohit Malshe wrote:
> > Dear all, 
> > 
> > I want to use a system in which 
> > 
> > Epsilon AA = 1 and Epsilon BB = 0.5.  
> > 
> > But I want to use Epsilon AB = 1.5. 
> > 
> > How do I do that in gromacs? 
> > 
> > 
> 
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] How to do rdf with out normalization?

[Xiaoling Leng]

Hi all, I want to compute the Radial distribution function with out
normalization, using g_rdf.
Or in another word, I want use g_rdf to count the numbers of the times
that 2 groups in certain distances. How could I do that? Could I use
some method to change the option -norm in g_rdf which in default is
"yes" to "no"?

Thanks in advance.

Xiaoling Leng
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Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB

[Justin A. Lemkul]

Rohit Malshe wrote:
Dear all, 

I want to use a system in which 

Epsilon AA = 1 and Epsilon BB = 0.5.  

But I want to use Epsilon AB = 1.5. 

How do I do that in gromacs? 





http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

-Justin

--


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


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[gmx-users] Epsilon AA, Epsilon AB, Epsilon BB

[Rohit Malshe]

Dear all, 

I want to use a system in which 

Epsilon AA = 1 and Epsilon BB = 0.5.  

But I want to use Epsilon AB = 1.5. 

How do I do that in gromacs? 


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RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

[Berk Hess]

Hi,

I asked the authors of the gmx amber ports what the desired behavior would be.
For the time being I committed the fix, but it only gets activated when you have
the env.var. GMX_FFRTP_TER_RENAME set.

Berk

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Date: Tue, 24 Aug 2010 20:48:05 +0200








Hi,

I have made a fix, but am now wondering if we actually want to fix this.
HIE is not a standard pdb residue name.
A file with HIS-HIS-HIS would work.
HIE is an Amber name and in that case one might say that you should use:
NHIE-HIE-CHIE.
But I don't know what the Amber program would support for input.

PS NHIE is now listed incorrectly as NHISE in residuetypes.dat,
so NHIE-HIE-CHIE won't work. I'll at least commit a fix for that.

Berk

From: alanwil...@gmail.com
Date: Tue, 24 Aug 2010 18:06:45 +0100
Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
To: gmx-users@gromacs.org

I am using gmx 4.5 d748b.
Thanks Berk, it seems to be working ... for DNA.
But this one is broken (and it was working before): HHH is tripetide 
Hie-Hie-Hie.


pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none
[snip]Identified residue HIE1 as a starting terminus.Identified residue HIE3 as 
a ending terminus.

8 out of 8 lines of specbond.dat converted successfully
---Program pdb2gmx, VERSION 
4.5-beta3-dev-20100824-d748bSource code file: 
/Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line: 916


Fatal error:There is a dangling bond at at least one of the terminal ends and 
the force field does not provide terminal entries or 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
Alan
On 24 August 2010 15:30, Berk Hess  wrote:







Hi,

I fixed it.
Thanks for the fast test and the complete instructions,

Berk

From: alanwil...@gmail.com
Date: Tue, 24 Aug 2010 15:22:34 +0100


To: gmx-users@gromacs.org
Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Hi there, in special Berk.


So pdb2gmx may be working with HIS and variants for oplsaa but now, something 
that was working before is failing:
wget -c "http://www.pdbe.org/download/1BNA"; -O 1BNA.pdb



grep 'ATOM  ' 1BNA.pdb >| DNA.pdb
cat << EOF >| SPE.mdpdefine = -DFLEXIBLEintegrator   = mdnsteps 
  = 0



dt   = 0.001constraints  = noneemtol
= 10.0emstep   = 0.01nstcomm  = 
1ns_type  = simple



nstlist  = 0rlist= 0rcoulomb
 = 0rvdw = 0Tcoupl   = noPcoupl 
  = no



gen_vel  = nonstxout  = 1pbc
  = nonstlog = 1nstenergy = 1nstvout = 1nstfout = 1nstxtcout = 1



comm_mode = ANGULARcontinuation = yesEOF
pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p 
DnaAmberSBGMX45[snip]



8 out of 8 lines of specbond.dat converted successfully[1]42209 
segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb 
-water none -p 
with 5e347 it worded fine, i.e, it opens files




Opening force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arnOpening
 force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn



Opening force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn
and proceed.
Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate




Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<





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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate


Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<



-- 
gmx-users maili

Re: [gmx-users] Incorrect C-terminal in peptide starting with GLY

[Krzysztof Kuczera]

Thank you
Krzysztof

Berk Hess wrote:

Hi,

I fixed it for the next beta release.
If you need it now, change on line 1574 (my latest version) of 
src/kernel/pdb2gmx.c

cc->r_start to cc->r_end, or get the 4.5 version from git.

Berk

Date: Tue, 24 Aug 2010 09:21:44 -0500
From: kkucz...@ku.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Incorrect C-terminal in peptide starting with GLY

Hi gmx-users
I am trying to set up a simulation of a 16-residue peptide that starts 
with GLY and ends with GLU
(PDB attached) using OPLS-AA/L and gromacs-4.5-beta3. Here is the 
pdb2gmx command
 
pdb2gmx -inter -ignh -f b-hp41-56.pdb -p peptide.top -o peptide.gro
 
the ff, water, ionization state selection goes well,

 I get a selection of N-terminals that includes GLY-NH3+ which is fine
but then the selection of C-terminals does not have COO-, but only GLY-COO-
- as a result the C-terminal GLU ends up with incorrect charge and qtot 
is not an integer
 
Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ...
 
Could someone suggest a fix for this ?
 
Regards

Krzysztof
 
--

Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html 

 
 
  

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--
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html


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RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

[Berk Hess]

Hi,

I have made a fix, but am now wondering if we actually want to fix this.
HIE is not a standard pdb residue name.
A file with HIS-HIS-HIS would work.
HIE is an Amber name and in that case one might say that you should use:
NHIE-HIE-CHIE.
But I don't know what the Amber program would support for input.

PS NHIE is now listed incorrectly as NHISE in residuetypes.dat,
so NHIE-HIE-CHIE won't work. I'll at least commit a fix for that.

Berk

From: alanwil...@gmail.com
Date: Tue, 24 Aug 2010 18:06:45 +0100
Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
To: gmx-users@gromacs.org

I am using gmx 4.5 d748b.
Thanks Berk, it seems to be working ... for DNA.
But this one is broken (and it was working before): HHH is tripetide 
Hie-Hie-Hie.


pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none
[snip]Identified residue HIE1 as a starting terminus.Identified residue HIE3 as 
a ending terminus.

8 out of 8 lines of specbond.dat converted successfully
---Program pdb2gmx, VERSION 
4.5-beta3-dev-20100824-d748bSource code file: 
/Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line: 916


Fatal error:There is a dangling bond at at least one of the terminal ends and 
the force field does not provide terminal entries or 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
Alan
On 24 August 2010 15:30, Berk Hess  wrote:







Hi,

I fixed it.
Thanks for the fast test and the complete instructions,

Berk

From: alanwil...@gmail.com
Date: Tue, 24 Aug 2010 15:22:34 +0100


To: gmx-users@gromacs.org
Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Hi there, in special Berk.


So pdb2gmx may be working with HIS and variants for oplsaa but now, something 
that was working before is failing:
wget -c "http://www.pdbe.org/download/1BNA"; -O 1BNA.pdb



grep 'ATOM  ' 1BNA.pdb >| DNA.pdb
cat << EOF >| SPE.mdpdefine = -DFLEXIBLEintegrator   = mdnsteps 
  = 0



dt   = 0.001constraints  = noneemtol
= 10.0emstep   = 0.01nstcomm  = 
1ns_type  = simple



nstlist  = 0rlist= 0rcoulomb
 = 0rvdw = 0Tcoupl   = noPcoupl 
  = no



gen_vel  = nonstxout  = 1pbc
  = nonstlog = 1nstenergy = 1nstvout = 1nstfout = 1nstxtcout = 1



comm_mode = ANGULARcontinuation = yesEOF
pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p 
DnaAmberSBGMX45[snip]



8 out of 8 lines of specbond.dat converted successfully[1]42209 
segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb 
-water none -p 
with 5e347 it worded fine, i.e, it opens files




Opening force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arnOpening
 force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn



Opening force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn
and proceed.
Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate




Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<





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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate


Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<



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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

There are 168 atom types in my system, 2 molecules comprising of 84
atoms each. The average temperature is 600 K but there are large
fluctuations ca ~100 K, which I assume is expected with such a smal
system. Ill check the energies



I would think it possible, even likely, that the thermostat is driving the 
behavior of your system, since it contains so few atoms.  Do check to see if 
temperature spikes correlate with movement of your pull_group to one side of the 
sampling window.  If it is the problem, try a different thermostat (or at least 
longer tau_t with N-H), and/or a substantially stronger pull_k1 if you're sure 
you need/want N-H as your thermostat.


I certainly agree with Chris' proposed test with two water molecules.  If you 
see the same thing, I'm even more confident that I'm right :)


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

O.K Thanks

My apologies for not stating earlier that I had the box dimensions set
to zero but I thought that when you set pbc = no and ns_type = simple
that "ignore the box" (from manual) was implemented.


Indeed.

How many atoms are in your system?  How well-conserved is the
temperature?  I imagine that if you only have a few atoms (relative to
a normal condensed-phase system), the species involved would be fairly
strongly impacted by the (potentially) wide oscillations of the
Nose-Hoover thermostat.  Maybe the thermostat is kicking your system
around?  Check the relevant energies and see if they sync up with the
configurations moving back and forth.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.


You have a box of zero size?  That doesn't make any sense to me, and I
doubt that such a setup plays nice with the MD code.  Frankly, I don't
see how it worked at all.

What if you place your system in a big box, no PBC, cutoffs = 0,
etc? Does that give you a sensible result?


Cheers

P.S I have plotted the pullx.xvg files for the distances between the
COMs of the molecules in the problematic windows. As was the case with
plotting with g_dist there is significant population of the at the
extremities of the window compared to that around the average r0.


Then technically, the average is probably fine, so the pull code is
satisfied. The sampling is clearly messed up for some reason.  Keep
digging :)

-Justin


Justin A. Lemkul wrote:

chris.ne...@utoronto.ca wrote:

I have seen this before, and there are a few possible reasons, but
I'm still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).


It's really hard to help you when we have to guess what the problem
looks like... or perhaps you posted it and I missed it?

The histogram was posted several days ago:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html

The attachment link is:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin




-Justin


-- original message --

O.K thanks anyway


Justin A. Lemkul
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html




Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm,
but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.








--


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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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

[Alan]

I am using gmx 4.5 d748b.

Thanks Berk, it seems to be working ... for DNA.

But this one is broken (and it was working before): HHH is tripetide
Hie-Hie-Hie.

pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none

[snip]
Identified residue HIE1 as a starting terminus.
Identified residue HIE3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

---
Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748b
Source code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line:
916

Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or 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

Alan

On 24 August 2010 15:30, Berk Hess  wrote:

>  Hi,
>
> I fixed it.
> Thanks for the fast test and the complete instructions,
>
> Berk
>
> --
> From: alanwil...@gmail.com
> Date: Tue, 24 Aug 2010 15:22:34 +0100
> To: gmx-users@gromacs.org
> Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
>
>
> Hi there, in special Berk.
>
> So pdb2gmx may be working with HIS and variants for oplsaa but now,
> something that was working before is failing:
>
> wget -c "http://www.pdbe.org/download/1BNA"; -O 1BNA.pdb
> grep 'ATOM  ' 1BNA.pdb >| DNA.pdb
>
> cat << EOF >| SPE.mdp
> define = -DFLEXIBLE
> integrator   = md
> nsteps   = 0
> dt   = 0.001
> constraints  = none
> emtol= 10.0
> emstep   = 0.01
> nstcomm  = 1
> ns_type  = simple
> nstlist  = 0
> rlist= 0
> rcoulomb = 0
> rvdw = 0
> Tcoupl   = no
> Pcoupl   = no
> gen_vel  = no
> nstxout  = 1
> pbc  = no
> nstlog = 1
> nstenergy = 1
> nstvout = 1
> nstfout = 1
> nstxtcout = 1
> comm_mode = ANGULAR
> continuation = yes
> EOF
>
> pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p
> DnaAmberSBGMX45
> [snip]
> 8 out of 8 lines of specbond.dat converted successfully
> [1]42209 segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb
> -ff amber99sb -water none -p
>
> with 5e347 it worded fine, i.e, it opens files
>
> Opening force field file
> /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn
> Opening force field file
> /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn
> Opening force field file
> /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn
>
> and proceed.
>
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
>
> -- gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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[gmx-users] pbc atom

[chris . neale]

Dear Gavin:

What happens if you replace your reference group by a single water  
molecule and your pulled group by a single water molecule and run the  
2.35 nm simulation again. Do you get the same two-peaked histogram?  
What about if you use a system with a single water for the reference  
and your regular pulled group?


You should not need to run 100 ns to get an idea about the shape of  
that histogram so it should be a quick test. This is usually how I  
figure things out -- see how much I can reduce the complexity and  
maintain the problem.


Chris.


-- original message --

Hi Chris

I have generated a histogram from the my.data file and i get a histogram
with the exact same profile as that generated from g_wham. Also on
comparison of the dx, dy, dz values in the g_dist file with the vaules
in the pullx.xvg file I notice that the magnitudes of the vectors are
identical but their signs are opposite. e.g.
g_dist file
-2.2756047   -0.03699810.3126130

pullx.xvg file
2.2756  0.036998-0.312613

Cheers

Gavin

Please note that there is a significantly more interaction between the
molecules below 2 nm whereas above they interact very weakly (from
viewing the trajectories)



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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Hi Chris

I have generated a histogram from the my.data file and i get a histogram
with the exact same profile as that generated from g_wham. Also on
comparison of the dx, dy, dz values in the g_dist file with the vaules
in the pullx.xvg file I notice that the magnitudes of the vectors are
identical but their signs are opposite. e.g.
g_dist file
-2.2756047   -0.03699810.3126130

pullx.xvg file
2.2756  0.036998-0.312613

Cheers

Gavin

Please note that there is a significantly more interaction between the
molecules below 2 nm whereas above they interact very weakly (from
viewing the trajectories)


chris.ne...@utoronto.ca wrote:
> Yup, just got the link. Thank you for posting, and sorry that I missed
> it. It seems possible that Justin is correct and you'll get good data
> if you take it out of the pullx.xvg file (perhaps the g_dist tool is
> wrapping pbc for you).
>
> 1. How big is your box definition in your .gro file?
>
> You are right that you need the actual distance, which is not provided
> directly. I think you want this (assuming that cols 5,6,7 give you the
> dx,dy,dz, which I believe that they do):
>
> cat pullx.xvg | grep -v '[#|@]' | awk '{print
> $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data
>
> 2. If you do this to a window > 2.0 nm and generate a histogram, do
> you still get two peaks?
>
> A quick look at the src/tools/gmx_dist.c file indicates that it should
> only apply periodicity if you give it a .tpr where PBC was applied --
> you can check this by comparing the dx, dy, dz out of g_dist with the
> values in pullx.xvg
>
> If the problem is not solved here, then you can send me off-list all
> the files needed to run a window around 2.5 nm plus all the output
> that you have obtained from a single run and I'll take a look if you
> wish. If you'd rather not do that and there are still problems, then
> perhaps you can post a step by step from the beginning where you copy
> and paste absolutely all of your commands (e.g. paste the *exact*
> grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and
> the last line in your starting .gro file.
>
> Chris.
>
> -- original message --
>
> [gmx-users] pbc atom
> Gavin Melaugh gmelaugh01 at qub.ac.uk
> Tue Aug 24 17:19:45 CEST 2010
>
> * Previous message: [gmx-users] pbc atom
> * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> Hi Chris
>
> Yeah I posted the histograms a few days ago as Justin said. Did you get
> the link?
>
> Gavin
> chris.neale at utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but I'm
>> still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
>>
>> -- original message --
>>
>> O.K thanks anyway
>>
>>
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>
>>
>>>
>>>
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm, but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>
>

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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Chris

The box dimensions that I type at the bottom of the .gro file are
0.0 0.0 0.0

In regards to the other points you made I'll get back to you as soon as
I can

Many Thanks

Gavin
chris.ne...@utoronto.ca wrote:
> Yup, just got the link. Thank you for posting, and sorry that I missed
> it. It seems possible that Justin is correct and you'll get good data
> if you take it out of the pullx.xvg file (perhaps the g_dist tool is
> wrapping pbc for you).
>
> 1. How big is your box definition in your .gro file?
>
> You are right that you need the actual distance, which is not provided
> directly. I think you want this (assuming that cols 5,6,7 give you the
> dx,dy,dz, which I believe that they do):
>
> cat pullx.xvg | grep -v '[#|@]' | awk '{print
> $1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data
>
> 2. If you do this to a window > 2.0 nm and generate a histogram, do
> you still get two peaks?
>
> A quick look at the src/tools/gmx_dist.c file indicates that it should
> only apply periodicity if you give it a .tpr where PBC was applied --
> you can check this by comparing the dx, dy, dz out of g_dist with the
> values in pullx.xvg
>
> If the problem is not solved here, then you can send me off-list all
> the files needed to run a window around 2.5 nm plus all the output
> that you have obtained from a single run and I'll take a look if you
> wish. If you'd rather not do that and there are still problems, then
> perhaps you can post a step by step from the beginning where you copy
> and paste absolutely all of your commands (e.g. paste the *exact*
> grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and
> the last line in your starting .gro file.
>
> Chris.
>
> -- original message --
>
> [gmx-users] pbc atom
> Gavin Melaugh gmelaugh01 at qub.ac.uk
> Tue Aug 24 17:19:45 CEST 2010
>
> * Previous message: [gmx-users] pbc atom
> * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> Hi Chris
>
> Yeah I posted the histograms a few days ago as Justin said. Did you get
> the link?
>
> Gavin
> chris.neale at utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but I'm
>> still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
>>
>> -- original message --
>>
>> O.K thanks anyway
>>
>>
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>
>>
>>>
>>>
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm, but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>
>

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Re: [gmx-users] pbc atom

[Gavin Melaugh]

There are 168 atom types in my system, 2 molecules comprising of 84
atoms each. The average temperature is 600 K but there are large
fluctuations ca ~100 K, which I assume is expected with such a smal
system. Ill check the energies

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> O.K Thanks
>>
>> My apologies for not stating earlier that I had the box dimensions set
>> to zero but I thought that when you set pbc = no and ns_type = simple
>> that "ignore the box" (from manual) was implemented.
>>
>
> Indeed.
>
> How many atoms are in your system?  How well-conserved is the
> temperature?  I imagine that if you only have a few atoms (relative to
> a normal condensed-phase system), the species involved would be fairly
> strongly impacted by the (potentially) wide oscillations of the
> Nose-Hoover thermostat.  Maybe the thermostat is kicking your system
> around?  Check the relevant energies and see if they sync up with the
> configurations moving back and forth.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Justin

 In regard to my query regarding the cut-offs at zero with no pbc. I
 assume its is fine to have box dimensions (0 0 0) to comply with the
 definition of a vacuum simulation. I am just worried that there may be
 some default cut-off that I am not aware of.

>>> You have a box of zero size?  That doesn't make any sense to me, and I
>>> doubt that such a setup plays nice with the MD code.  Frankly, I don't
>>> see how it worked at all.
>>>
>>> What if you place your system in a big box, no PBC, cutoffs = 0,
>>> etc? Does that give you a sensible result?
>>>
 Cheers

 P.S I have plotted the pullx.xvg files for the distances between the
 COMs of the molecules in the problematic windows. As was the case with
 plotting with g_dist there is significant population of the at the
 extremities of the window compared to that around the average r0.

>>> Then technically, the average is probably fine, so the pull code is
>>> satisfied. The sampling is clearly messed up for some reason.  Keep
>>> digging :)
>>>
>>> -Justin
>>>
 Justin A. Lemkul wrote:
> chris.ne...@utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but
>> I'm still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>>
>>
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
> The histogram was posted several days ago:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html
>
> The attachment link is:
>
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin
>
>
>
>
> -Justin
>
>> -- original message --
>>
>> O.K thanks anyway
>>
>>
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>
>>
>>
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm,
 but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>>> Sorry, no clue.
>>>

>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

O.K Thanks

My apologies for not stating earlier that I had the box dimensions set
to zero but I thought that when you set pbc = no and ns_type = simple
that "ignore the box" (from manual) was implemented.



Indeed.

How many atoms are in your system?  How well-conserved is the temperature?  I 
imagine that if you only have a few atoms (relative to a normal condensed-phase 
system), the species involved would be fairly strongly impacted by the 
(potentially) wide oscillations of the Nose-Hoover thermostat.  Maybe the 
thermostat is kicking your system around?  Check the relevant energies and see 
if they sync up with the configurations moving back and forth.


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Justin

In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.


You have a box of zero size?  That doesn't make any sense to me, and I
doubt that such a setup plays nice with the MD code.  Frankly, I don't
see how it worked at all.

What if you place your system in a big box, no PBC, cutoffs = 0, etc? 
Does that give you a sensible result?



Cheers

P.S I have plotted the pullx.xvg files for the distances between the
COMs of the molecules in the problematic windows. As was the case with
plotting with g_dist there is significant population of the at the
extremities of the window compared to that around the average r0.


Then technically, the average is probably fine, so the pull code is
satisfied. The sampling is clearly messed up for some reason.  Keep
digging :)

-Justin


Justin A. Lemkul wrote:

chris.ne...@utoronto.ca wrote:

I have seen this before, and there are a few possible reasons, but
I'm still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).

It's really hard to help you when we have to guess what the problem
looks like... or perhaps you posted it and I missed it?

The histogram was posted several days ago:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html

The attachment link is:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin



-Justin


-- original message --

O.K thanks anyway


Justin A. Lemkul
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html



Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.








--


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] pbc atom

[chris . neale]

Yup, just got the link. Thank you for posting, and sorry that I missed  
it. It seems possible that Justin is correct and you'll get good data  
if you take it out of the pullx.xvg file (perhaps the g_dist tool is  
wrapping pbc for you).


1. How big is your box definition in your .gro file?

You are right that you need the actual distance, which is not provided  
directly. I think you want this (assuming that cols 5,6,7 give you the  
dx,dy,dz, which I believe that they do):


cat pullx.xvg | grep -v '[#|@]' | awk '{print  
$1,sqrt($5*$5+$6*$6+$7*$7)}' > my.data


2. If you do this to a window > 2.0 nm and generate a histogram, do  
you still get two peaks?


A quick look at the src/tools/gmx_dist.c file indicates that it should  
only apply periodicity if you give it a .tpr where PBC was applied --  
you can check this by comparing the dx, dy, dz out of g_dist with the  
values in pullx.xvg


If the problem is not solved here, then you can send me off-list all  
the files needed to run a window around 2.5 nm plus all the output  
that you have obtained from a single run and I'll take a look if you  
wish. If you'd rather not do that and there are still problems, then  
perhaps you can post a step by step from the beginning where you copy  
and paste absolutely all of your commands (e.g. paste the *exact*  
grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and  
the last line in your starting .gro file.


Chris.

-- original message --

[gmx-users] pbc atom
Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Aug 24 17:19:45 CEST 2010

* Previous message: [gmx-users] pbc atom
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Hi Chris

Yeah I posted the histograms a few days ago as Justin said. Did you get
the link?

Gavin
chris.neale at utoronto.ca wrote:

I have seen this before, and there are a few possible reasons, but I'm
still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
It's really hard to help you when we have to guess what the problem
looks like... or perhaps you posted it and I missed it?

-- original message --

O.K thanks anyway


Justin A. Lemkul
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html




Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.




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Re: [gmx-users] pbc atom

[Gavin Melaugh]

O.K Thanks

My apologies for not stating earlier that I had the box dimensions set
to zero but I thought that when you set pbc = no and ns_type = simple
that "ignore the box" (from manual) was implemented.

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Justin
>>
>> In regard to my query regarding the cut-offs at zero with no pbc. I
>> assume its is fine to have box dimensions (0 0 0) to comply with the
>> definition of a vacuum simulation. I am just worried that there may be
>> some default cut-off that I am not aware of.
>>
>
> You have a box of zero size?  That doesn't make any sense to me, and I
> doubt that such a setup plays nice with the MD code.  Frankly, I don't
> see how it worked at all.
>
> What if you place your system in a big box, no PBC, cutoffs = 0, etc? 
> Does that give you a sensible result?
>
>> Cheers
>>
>> P.S I have plotted the pullx.xvg files for the distances between the
>> COMs of the molecules in the problematic windows. As was the case with
>> plotting with g_dist there is significant population of the at the
>> extremities of the window compared to that around the average r0.
>>
>
> Then technically, the average is probably fine, so the pull code is
> satisfied. The sampling is clearly messed up for some reason.  Keep
> digging :)
>
> -Justin
>
>> Justin A. Lemkul wrote:
>>>
>>> chris.ne...@utoronto.ca wrote:
 I have seen this before, and there are a few possible reasons, but
 I'm still waiting to see that histogram with two peaks
 (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).

 It's really hard to help you when we have to guess what the problem
 looks like... or perhaps you posted it and I missed it?
>>> The histogram was posted several days ago:
>>>
>>> http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html
>>>
>>> The attachment link is:
>>>
>>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin
>>>
>>>
>>>
>>> -Justin
>>>
 -- original message --

 O.K thanks anyway


 Justin A. Lemkul
 wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html


>
> Gavin Melaugh wrote:
>> Thanks Justin
>>
>> Have you any idea why when generating umbrella histograms for the
>> pmf I
>> would get two peaks in the histograms above a distance of 2 nm, but
>> below 2 nm I get well behaved histograms that lead to a very
>> good profile in the pmf. To the best of my knowledge the
>> configurations
>> are all very well equilibrated at their respective COM distances.
>> Umbrella sampling is performed on all windows using a force
>> constant of
>> 1000 kj/mol at 600 K.
>>
> Sorry, no clue.
>

>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

Justin

In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.



You have a box of zero size?  That doesn't make any sense to me, and I doubt 
that such a setup plays nice with the MD code.  Frankly, I don't see how it 
worked at all.


What if you place your system in a big box, no PBC, cutoffs = 0, etc?  Does that 
give you a sensible result?



Cheers

P.S I have plotted the pullx.xvg files for the distances between the
COMs of the molecules in the problematic windows. As was the case with
plotting with g_dist there is significant population of the at the
extremities of the window compared to that around the average r0.



Then technically, the average is probably fine, so the pull code is satisfied. 
The sampling is clearly messed up for some reason.  Keep digging :)


-Justin


Justin A. Lemkul wrote:


chris.ne...@utoronto.ca wrote:

I have seen this before, and there are a few possible reasons, but
I'm still waiting to see that histogram with two peaks
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
It's really hard to help you when we have to guess what the problem
looks like... or perhaps you posted it and I missed it?

The histogram was posted several days ago:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html

The attachment link is:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin


-Justin


-- original message --

O.K thanks anyway


Justin A. Lemkul
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html



Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.








--


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] pbc atom

[Gavin Melaugh]

Justin

In regard to my query regarding the cut-offs at zero with no pbc. I
assume its is fine to have box dimensions (0 0 0) to comply with the
definition of a vacuum simulation. I am just worried that there may be
some default cut-off that I am not aware of.

Cheers

P.S I have plotted the pullx.xvg files for the distances between the
COMs of the molecules in the problematic windows. As was the case with
plotting with g_dist there is significant population of the at the
extremities of the window compared to that around the average r0.

Justin A. Lemkul wrote:
>
>
> chris.ne...@utoronto.ca wrote:
>> I have seen this before, and there are a few possible reasons, but
>> I'm still waiting to see that histogram with two peaks
>> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
>> It's really hard to help you when we have to guess what the problem
>> looks like... or perhaps you posted it and I missed it?
>
> The histogram was posted several days ago:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html
>
> The attachment link is:
>
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin
>
>
> -Justin
>
>>
>> -- original message --
>>
>> O.K thanks anyway
>>
>>
>> Justin A. Lemkul
>> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>>
>>>
>>>
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm, but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>>>
>>> Sorry, no clue.
>>>
>>
>>
>

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Re: [gmx-users] pbc atom

[Gavin Melaugh]

Hi Chris

Yeah I posted the histograms a few days ago as Justin said. Did you get
the link?

Gavin
chris.ne...@utoronto.ca wrote:
> I have seen this before, and there are a few possible reasons, but I'm
> still waiting to see that histogram with two peaks
> (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html).
> It's really hard to help you when we have to guess what the problem
> looks like... or perhaps you posted it and I missed it?
>
> -- original message --
>
> O.K thanks anyway
>
>
> Justin A. Lemkul
> wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html
>
>>
>>
>> Gavin Melaugh wrote:
>>> Thanks Justin
>>>
>>> Have you any idea why when generating umbrella histograms for the pmf I
>>> would get two peaks in the histograms above a distance of 2 nm, but
>>> below 2 nm I get well behaved histograms that lead to a very
>>> good profile in the pmf. To the best of my knowledge the configurations
>>> are all very well equilibrated at their respective COM distances.
>>> Umbrella sampling is performed on all windows using a force constant of
>>> 1000 kj/mol at 600 K.
>>>
>>
>> Sorry, no clue.
>>
>
>

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Re: [gmx-users] help with git

[Mark Abraham]

- Original Message -
From: Alan 
Date: Wednesday, August 25, 2010 0:10
Subject: Re: [gmx-users] help with git
To: Discussion list for GROMACS users 

> Sorry if confused... because I am *really* confused too with git.
> Anyway, I started anew again and it seems to be working now.> 
> So I clone gmx:> 
> git clone git://git.gromacs.org/gromacs.git  > cd gromacs> git branch> * 
> master> git pull> Already up-to-date.> # now I want to move to 
> 'release-4-5-patch' branch> git checkout -t origin/release-4-5-patches 

If you read the help/manpage for "git checkout" 
(http://www.kernel.org/pub/software/scm/git/docs/git-checkout.html), then you 
will realise you don't want "-t". Tracking of upstream branches is normally set 
up when the branch is created. Rarely, having created a branch, you now want it 
track something upstream, and you can do that too. However, unless you're 
creating branches don't worry about it. These branches already exist - see "git 
branch -a".

I think you just want "git checkout release-4-5-patches" from a fresh clone.

  > Branch release-4-5-patches set up to track remote branch 
release-4-5-patches from origin.> Switched to a new branch 
'release-4-5-patches'> git branch >   master>   * release-4-5-patches> git pull 
> Already up-to-date.> # now I want to go back to master> git checkout -t 
origin/master > fatal: git checkout: branch master already exists

-t is trying to create the branch. So don't do that.

  > git branch   >   master> * release-4-5-patches> # didn't 
change, let's try another command (and here starts my 'guessing' experiment)  > 
git checkout master> Switched to branch 'master'> # nice it works!

Sure.

Mark

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

chris.ne...@utoronto.ca wrote:
I have seen this before, and there are a few possible reasons, but I'm 
still waiting to see that histogram with two peaks 
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). 
It's really hard to help you when we have to guess what the problem 
looks like... or perhaps you posted it and I missed it?


The histogram was posted several days ago:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053317.html

The attachment link is:

http://lists.gromacs.org/pipermail/gmx-users/attachments/20100820/fc07fb81/histo.ps.bin

-Justin



-- original message --

O.K thanks anyway


Justin A. Lemkul 
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html



Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.



Sorry, no clue.






--


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] pbc atom

[chris . neale]

I have seen this before, and there are a few possible reasons, but I'm  
still waiting to see that histogram with two peaks  
(http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). It's  
really hard to help you when we have to guess what the problem looks  
like... or perhaps you posted it and I missed it?


-- original message --

O.K thanks anyway


Justin A. Lemkul  
wrote:http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html



Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.



Sorry, no clue.




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Re: [gmx-users] Different hexane/water surface tensi ons for different ensembles (NVT and NAɣT)

[Pedro Alexandre de Araújo Gomes Lapido Loureiro]

It is probably due to the fact that z-dimensions are different in your two
systems.
Check "Surface tension coupling" in the manual.

Cheers,

Pedro.

2010/8/24 Ozge Engin 

> Hi all,
>
> I am trying to calculate the surface tension of hexane/water interface. I
> used two different ensembles: constant particle, volume, temperature (NVT),
> and constant area but let the box fluctuate on the z axis (NAɣT). Everything
> except the ensemble is the same for two simulation set-up s: number of
> molecules, temperature, temperature coupling, electrostatic and VDW
> interaction schemes, cut-off etc.
>
> I found a value close to the experimental one (52 dyn/cm) by using the NVT
> ensemble. In order to check whether it is dependent on the system size, I
> tried different sized systems, but it does not change. The results were the
> same within the error bars, which is good. However, when I attempt to change
> the ensemble to NAɣT I found different result. It is around 48 (1) dyn/cm.
> Actually, I expected to have the same values with the two ensembles, but
> not.
>
> Am I missing something that is straightforward?
>
> Regards
>
> --
> Ozge Engin
>  ★☆
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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RE: [gmx-users] Incorrect C-terminal in peptide starting with GLY

[Berk Hess]

Hi,

I fixed it for the next beta release.
If you need it now, change on line 1574 (my latest version) of 
src/kernel/pdb2gmx.c
cc->r_start to cc->r_end, or get the 4.5 version from git.

Berk

Date: Tue, 24 Aug 2010 09:21:44 -0500
From: kkucz...@ku.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Incorrect C-terminal in peptide starting with GLY

Hi gmx-users
I am trying to set up a simulation of a 16-residue peptide that starts 
with GLY and ends with GLU
(PDB attached) using OPLS-AA/L and gromacs-4.5-beta3. Here is the 
pdb2gmx command
 
pdb2gmx -inter -ignh -f b-hp41-56.pdb -p peptide.top -o peptide.gro
 
the ff, water, ionization state selection goes well,
 I get a selection of N-terminals that includes GLY-NH3+ which is fine
but then the selection of C-terminals does not have COO-, but only GLY-COO-
- as a result the C-terminal GLU ends up with incorrect charge and qtot 
is not an integer
 
Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ...
 
Could someone suggest a fix for this ?
 
Regards
Krzysztof
 
-- 
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
 
 

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[gmx-users] Incorrect C-terminal in peptide starting with GLY

[Krzysztof Kuczera]

Hi gmx-users
I am trying to set up a simulation of a 16-residue peptide that starts 
with GLY and ends with GLU
(PDB attached) using OPLS-AA/L and gromacs-4.5-beta3. Here is the 
pdb2gmx command


pdb2gmx -inter -ignh -f b-hp41-56.pdb -p peptide.top -o peptide.gro

the ff, water, ionization state selection goes well,
I get a selection of N-terminals that includes GLY-NH3+ which is fine
but then the selection of C-terminals does not have COO-, but only GLY-COO-
- as a result the C-terminal GLU ends up with incorrect charge and qtot 
is not an integer


Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ...

Could someone suggest a fix for this ?

Regards
Krzysztof

--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html


ATOM611  N   GLY A  41   8.275   2.108  -6.519  1.00  0.22   N  
ATOM612  CA  GLY A  41   8.583   1.213  -7.670  1.00  0.27   C  
ATOM613  C   GLY A  41   7.287   0.722  -8.317  1.00  0.10   C  
ATOM614  O   GLY A  41   6.571   1.487  -8.932  1.00  0.15   O  
ATOM615  H   GLY A  41   7.358   2.180  -6.181  1.00  0.20   H  
ATOM616  HA2 GLY A  41   9.164   1.755  -8.401  1.00  0.46   H  
ATOM617  HA3 GLY A  41   9.152   0.363  -7.320  1.00  0.35   H  
ATOM618  N   GLU A  42   7.014  -0.545  -8.162  1.00  0.18   N  
ATOM619  CA  GLU A  42   5.765  -1.105  -8.753  1.00  0.19   C  
ATOM620  C   GLU A  42   4.692  -1.213  -7.673  1.00  0.15   C  
ATOM621  O   GLU A  42   5.001  -1.443  -6.522  1.00  0.17   O  
ATOM622  CB  GLU A  42   6.054  -2.489  -9.311  1.00  0.38   C  
ATOM623  CG  GLU A  42   7.242  -2.407 -10.272  1.00  0.46   C  
ATOM624  CD  GLU A  42   6.818  -2.934 -11.644  1.00  1.51   C  
ATOM625  OE1 GLU A  42   6.254  -2.140 -12.379  1.00  2.54   O  
ATOM626  OE2 GLU A  42   7.081  -4.102 -11.880  1.00  1.65   O  
ATOM627  H   GLU A  42   7.623  -1.124  -7.656  1.00  0.33   H  
ATOM628  HA  GLU A  42   5.417  -0.463  -9.544  1.00  0.19   H  
ATOM629  HB2 GLU A  42   6.286  -3.157  -8.500  1.00  0.41   H  
ATOM630  HB3 GLU A  42   5.185  -2.857  -9.837  1.00  0.46   H  
ATOM631  HG2 GLU A  42   7.565  -1.381 -10.368  1.00  0.70   H  
ATOM632  HG3 GLU A  42   8.058  -3.005  -9.896  1.00  0.59   H  
ATOM633  N   TRP A  43   3.457  -1.056  -8.070  1.00  0.15   N  
ATOM634  CA  TRP A  43   2.343  -1.130  -7.075  1.00  0.12   C  
ATOM635  C   TRP A  43   1.302  -2.160  -7.508  1.00  0.11   C  
ATOM636  O   TRP A  43   0.940  -2.232  -8.665  1.00  0.12   O  
ATOM637  CB  TRP A  43   1.697   0.244  -6.975  1.00  0.12   C  
ATOM638  CG  TRP A  43   2.573   1.127  -6.086  1.00  0.12   C  
ATOM639  CD1 TRP A  43   3.740   1.623  -6.479  1.00  0.15   C  
ATOM640  CD2 TRP A  43   2.306   1.476  -4.830  1.00  0.11   C  
ATOM641  NE1 TRP A  43   4.179   2.297  -5.406  1.00  0.14   N  
ATOM642  CE2 TRP A  43   3.336   2.255  -4.322  1.00  0.12   C  
ATOM643  CE3 TRP A  43   1.220   1.177  -4.011  1.00  0.11   C  
ATOM644  CZ2 TRP A  43   3.284   2.724  -3.026  1.00  0.13   C  
ATOM645  CZ3 TRP A  43   1.176   1.650  -2.715  1.00  0.12   C  
ATOM646  CH2 TRP A  43   2.205   2.421  -2.224  1.00  0.13   C  
ATOM647  H   TRP A  43   3.261  -0.889  -9.016  1.00  0.19   H  
ATOM648  HA  TRP A  43   2.734  -1.406  -6.112  1.00  0.12   H  
ATOM649  HB2 TRP A  43   1.636   0.687  -7.958  1.00  0.13   H  
ATOM650  HB3 TRP A  43   0.710   0.160  -6.562  1.00  0.10   H  
ATOM651  HD1 TRP A  43   4.251   1.453  -7.418  1.00  0.17   H  
ATOM652  HE1 TRP A  43   5.032   2.779  -5.396  1.00  0.16   H  
ATOM653  HE3 TRP A  43   0.411   0.572  -4.379  1.00  0.11   H  
ATOM654  HZ2 TRP A  43   4.091   3.327  -2.639  1.00  0.14   H  
ATOM655  HZ3 TRP A  43   0.330   1.415  -2.085  1.00  0.14   H  
ATOM656  HH2 TRP A  43   2.169   2.784  -1.207  1.00  0.15   H  
ATOM657  N   THR A  44   0.846  -2.936  -6.556  1.00  0.08   N  
ATOM658  CA  THR A  44  -0.177  -3.982  -6.872  1.00  0.08   C  
ATOM659  C   THR A  44  -1.437  -3.780  -6.019  1.00  0.07   C  
ATOM660  O   THR A  44  -1.434  -3.037  -5.058  1.00  0.13   O  
ATOM661  CB  TH

RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

[Berk Hess]

Hi,

I fixed it.
Thanks for the fast test and the complete instructions,

Berk

From: alanwil...@gmail.com
Date: Tue, 24 Aug 2010 15:22:34 +0100
To: gmx-users@gromacs.org
Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Hi there, in special Berk.
So pdb2gmx may be working with HIS and variants for oplsaa but now, something 
that was working before is failing:
wget -c "http://www.pdbe.org/download/1BNA"; -O 1BNA.pdb

grep 'ATOM  ' 1BNA.pdb >| DNA.pdb
cat << EOF >| SPE.mdpdefine = -DFLEXIBLEintegrator   = mdnsteps 
  = 0

dt   = 0.001constraints  = noneemtol
= 10.0emstep   = 0.01nstcomm  = 
1ns_type  = simple

nstlist  = 0rlist= 0rcoulomb
 = 0rvdw = 0Tcoupl   = noPcoupl 
  = no

gen_vel  = nonstxout  = 1pbc
  = nonstlog = 1nstenergy = 1nstvout = 1nstfout = 1nstxtcout = 1

comm_mode = ANGULARcontinuation = yesEOF
pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p 
DnaAmberSBGMX45[snip]

8 out of 8 lines of specbond.dat converted successfully[1]42209 
segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb 
-water none -p 
with 5e347 it worded fine, i.e, it opens files


Opening force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arnOpening
 force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn

Opening force field file 
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn
and proceed.
Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate


Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<



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[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

[Alan]

Hi there, in special Berk.

So pdb2gmx may be working with HIS and variants for oplsaa but now,
something that was working before is failing:

wget -c "http://www.pdbe.org/download/1BNA"; -O 1BNA.pdb
grep 'ATOM  ' 1BNA.pdb >| DNA.pdb

cat << EOF >| SPE.mdp
define = -DFLEXIBLE
integrator   = md
nsteps   = 0
dt   = 0.001
constraints  = none
emtol= 10.0
emstep   = 0.01
nstcomm  = 1
ns_type  = simple
nstlist  = 0
rlist= 0
rcoulomb = 0
rvdw = 0
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 1
pbc  = no
nstlog = 1
nstenergy = 1
nstvout = 1
nstfout = 1
nstxtcout = 1
comm_mode = ANGULAR
continuation = yes
EOF

pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p
DnaAmberSBGMX45
[snip]
8 out of 8 lines of specbond.dat converted successfully
[1]42209 segmentation fault  pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb
-ff amber99sb -water none -p

with 5e347 it worded fine, i.e, it opens files

Opening force field file
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn
Opening force field file
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn
Opening force field file
/Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn

and proceed.

Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

O.K thanks Justine I'll look at these files and see if there is any
weirdness.
Just to make sure that there are no cut-off artefacts. If I  set the
cut-offs to zero as in the following mdp file; that does mean that I am
considering all electrostatic and LJ interactions between the molecules?
and not including them at all. I assume the former given that there are
both electrostatic and LJ energy values in the log and energy files.



Correct.

-Justin


Gavin

title   = Pull test
cpp =
include =
define  =
integrator  = md
nsteps  = 5000
dt  = 0.002
nstxout = 25
nstvout = 25
nstlog  = 25
nstenergy   = 5000
nstfout = 25
pbc = no
nstlist = 10
ns_type = simple
vdwtype = cut-off
rlist   = 0
rvdw_switch = 0
rvdw= 0
coulombtype = cut-off
rcoulomb= 0
tcoupl  = nose-hoover
tc_grps = system
tau_t   = 0.1
ref_t   = 600
gen_vel = no
gen_temp=
constraints = none
comm_mode   = angular
pull= umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_init1 = 2.59
pull_rate1 = 0.0
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000


Justin A. Lemkul wrote:


Gavin Melaugh wrote:

For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus) as supposed
to the displacement along a given vector component?


For diagnosing weird behavior, I would always start with the primary
data, not any post-processed interpretation of it.  Use the pullx.xvg
file.  Any weird changes in sign or sudden changes in magnitude would
indicate problems.  If you start manipulating the data, you may be
hiding the real reason for the problem.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM
distance
from the pullx.xvg file


That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
group, then displacement (dX,dY,dZ) of the pull group relative to the
reference.  Not all terms may be present, depending on the axis along
which you're pulling, i.e. if you only pull along Z, there will be two
terms in pullx.xvg - Z and dZ.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

I have looked at the movies but it's very hard to tell what's
going on
as I save teh trajectories every 25 steps for every 5000
step
simulation (100 ns). Ill look at them  again in more detail and post
back.


Plotting the pullx.xvg file(s) may be useful, too, to indicate where
any weird jumps or sudden changes in position might occur.  Mapping
that information back onto the trajectory could help focus your
attention.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

O.K thanks anyway


I saw the plots you posted during a conversation with Chris, but
I'll
ask the obvious anyway: have you watched the trajectories for
any of
the problematic windows?  It didn't seem like you had two
metastable
states, but maybe having a look at the movie would shed some
light on
what's going on.  I know that's the first thing I'd do.

-Justin


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for
the
pmf I
would get two peaks in the histograms above a distance of 2 nm,
but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM
distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull
code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the
output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start   
reference at

t=0
   07236
   172   360   4.290 4.290

why is this so?


grompp always assigns the numerical middle atom of a group as
the
PBC 

...unless over-ridden by providing a different value for
pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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

=

Re: [gmx-users] pbc atom

[Gavin Melaugh]

O.K thanks Justine I'll look at these files and see if there is any
weirdness.
Just to make sure that there are no cut-off artefacts. If I  set the
cut-offs to zero as in the following mdp file; that does mean that I am
considering all electrostatic and LJ interactions between the molecules?
and not including them at all. I assume the former given that there are
both electrostatic and LJ energy values in the log and energy files.

Gavin

title   = Pull test
cpp =
include =
define  =
integrator  = md
nsteps  = 5000
dt  = 0.002
nstxout = 25
nstvout = 25
nstlog  = 25
nstenergy   = 5000
nstfout = 25
pbc = no
nstlist = 10
ns_type = simple
vdwtype = cut-off
rlist   = 0
rvdw_switch = 0
rvdw= 0
coulombtype = cut-off
rcoulomb= 0
tcoupl  = nose-hoover
tc_grps = system
tau_t   = 0.1
ref_t   = 600
gen_vel = no
gen_temp=
constraints = none
comm_mode   = angular
pull= umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_init1 = 2.59
pull_rate1 = 0.0
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000


Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> For the umbrella sampling I am not pulling in any direction I am just
>> applying the umbrella potential so that two molecules can sample space
>> about a give value of r0 (COM distance). Maybe I am confused but should
>> I not plot the absolute value of the displacement (modulus) as supposed
>> to the displacement along a given vector component?
>>
>
> For diagnosing weird behavior, I would always start with the primary
> data, not any post-processed interpretation of it.  Use the pullx.xvg
> file.  Any weird changes in sign or sudden changes in magnitude would
> indicate problems.  If you start manipulating the data, you may be
> hiding the real reason for the problem.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 I always used g_dist to plot the COM distances because the pullx.xvg
 files doesn't give this value directly. Can you access the COM
 distance
 from the pullx.xvg file

>>> That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
>>> group, then displacement (dX,dY,dZ) of the pull group relative to the
>>> reference.  Not all terms may be present, depending on the axis along
>>> which you're pulling, i.e. if you only pull along Z, there will be two
>>> terms in pullx.xvg - Z and dZ.
>>>
>>> -Justin
>>>
 Gavin

 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Justin
>>
>> I have looked at the movies but it's very hard to tell what's
>> going on
>> as I save teh trajectories every 25 steps for every 5000
>> step
>> simulation (100 ns). Ill look at them  again in more detail and post
>> back.
>>
> Plotting the pullx.xvg file(s) may be useful, too, to indicate where
> any weird jumps or sudden changes in position might occur.  Mapping
> that information back onto the trajectory could help focus your
> attention.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>> Gavin Melaugh wrote:
 O.K thanks anyway

>>> I saw the plots you posted during a conversation with Chris, but
>>> I'll
>>> ask the obvious anyway: have you watched the trajectories for
>>> any of
>>> the problematic windows?  It didn't seem like you had two
>>> metastable
>>> states, but maybe having a look at the movie would shed some
>>> light on
>>> what's going on.  I know that's the first thing I'd do.
>>>
>>> -Justin
>>>
 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Thanks Justin
>>
>> Have you any idea why when generating umbrella histograms for
>> the
>> pmf I
>> would get two peaks in the histograms above a distance of 2 nm,
>> but
>> below 2 nm I get well behaved histograms that lead to a very
>> good profile in the pmf. To the best of my knowledge the
>> configurations
>> are all very well equilibrated at their respective COM
>> distances.
>> Umbrella sampling is performed on all windows using a force
>> constant of
>> 1000 kj/mol at 600 K.
>>
> Sorry, no clue.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>> Justin A. Lemkul wrote:
 Gavin Melaugh wrote:
> Hi all
>
> I am generating a series of configurations using the pull
> code to
> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
> output
> from grommp gives me info on pbc atom.
>
> Pull group  natoms  pbc atom  

Re: [gmx-users] help with git

[Alan]

Sorry if confused... because I am *really* confused too with git.

Anyway, I started anew again and it seems to be working now.

So I clone gmx:

git clone git://git.gromacs.org/gromacs.git
cd gromacs
git branch
* master
git pull
Already up-to-date.
# now I want to move to 'release-4-5-patch' branch
git checkout -t origin/release-4-5-patches
Branch release-4-5-patches set up to track remote branch release-4-5-patches
from origin.
Switched to a new branch 'release-4-5-patches'
git branch
  master
* release-4-5-patches
git pull
Already up-to-date.
# now I want to go back to master
git checkout -t origin/master
fatal: git checkout: branch master already exists
git branch
  master
* release-4-5-patches
# didn't change, let's try another command (and here starts my 'guessing'
experiment)
git checkout master
Switched to branch 'master'
# nice it works!

Thanks,

Alan

On 24 August 2010 14:14, Roland Schulz  wrote:

>
>
> On Tue, Aug 24, 2010 at 9:01 AM, Alan  wrote:
>
>> Ok, doing:
>>
>> git reset origin/release-4-5-patches
>> git checkout origin/release-4-5-patches
>>
> I'm confused what you are trying to do. But you are not supposed to
> checkout a remote branch.
>
>> git pull
>> Already up-to-date.
>>
>> restored the sanity of system.
>>
>> On 24 August 2010 13:52, Alan  wrote:
>>
>>> Thanks Carsten, but now nothing is not working, not even what was doing
>>> so:
>>>
>>> git reset --hard
>>> HEAD is now at 5e3473a Merge branch 'release-4-5-patches'
>>>  amadeus[2216]:~/workspace/gromacs% git checkout release-4-5-patches
>>> Already on 'release-4-5-patches'
>>> Your branch and 'origin/release-4-5-patches' have diverged,
>>> and have 37 and 31 different commit(s) each, respectively.
>>> amadeus[2217]:~/workspace/gromacs% git pull
>>> Auto-merging include/physics.h
>>> Auto-merging include/resall.h
>>> CONFLICT (content): Merge conflict in include/resall.h
>>> Auto-merging include/string2.h
>>> CONFLICT (content): Merge conflict in include/string2.h
>>> Auto-merging include/vec.h
>>> CONFLICT (content): Merge conflict in include/vec.h
>>> Auto-merging src/gmxlib/string2.c
>>> Auto-merging src/kernel/gen_vsite.c
>>> Auto-merging src/kernel/pdb2gmx.c
>>> Auto-merging src/kernel/pdb2top.c
>>> CONFLICT (content): Merge conflict in src/kernel/pdb2top.c
>>> Auto-merging src/kernel/resall.c
>>> Auto-merging src/kernel/ter_db.c
>>> Auto-merging src/tools/gmx_membed.c
>>> Automatic merge failed; fix conflicts and then commit the result.
>>> amadeus[2218]:~/workspace/gromacs%
>>>
>>>
>>>
>>> On 24 August 2010 12:10, Carsten Kutzner  wrote:
>>>
 On Aug 24, 2010, at 12:57 PM, Alan wrote:

 Hi there,

 I want to change from release-4-5-patches to master

 I am trying:

 git reset master
 git checkout master

 git pull
 error: Your local changes to 'include/resall.h' would be overwritten by
 merge.  Aborting.
 Please, commit your changes or stash them before you can merge.

 git stash
 Saved working directory and index state WIP on master: 5e3473a Merge
 branch 'release-4-5-patches'
 HEAD is now at 5e3473a Merge branch 'release-4-5-patches'

 But I don't want branch 'release-4-5-patches'!

 Indeed, I am finding git very annoying to use.

 All I wanted in svn lingo is to change to a branch and if there's
 conflict, ignore all changes in my side and revert any modification to
 what's in the repository.

 git reset --hard
 will remove all your modifications to that branch that are not checked
 in yet. You might
 want to save include/resall.h elsewhere if you still need your
 modifications.

 Then
 git checkout master

 will check out the master branch. You might need to "git pull" after you
 checked
 out the master so that you are up-to-date with the gromacs repository.

 Carsten


 Is it possible with git?

 Thanks,

 Alan


 --
 Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
 Department of Biochemistry, University of Cambridge.
 80 Tennis Court Road, Cambridge CB2 1GA, UK.
 >>http://www.bio.cam.ac.uk/~awd28<<
  --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php



 --
 Dr. Carsten Kutzner
 Max Planck Institute for Biophysical Chemistry
 Theoretical and Computational Biophysics
 Am Fassberg 11, 37077 Goettingen, Germany
 Tel. +49-551-2012313, Fax: +49-551-2012302
 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne





 --

 gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Different hexane/water surface tensions fo r different ensembles (NVT and NAɣT)

[Ozge Engin]

Hi all,

I am trying to calculate the surface tension of hexane/water interface. I
used two different ensembles: constant particle, volume, temperature (NVT),
and constant area but let the box fluctuate on the z axis (NAɣT). Everything
except the ensemble is the same for two simulation set-up s: number of
molecules, temperature, temperature coupling, electrostatic and VDW
interaction schemes, cut-off etc.

I found a value close to the experimental one (52 dyn/cm) by using the NVT
ensemble. In order to check whether it is dependent on the system size, I
tried different sized systems, but it does not change. The results were the
same within the error bars, which is good. However, when I attempt to change
the ensemble to NAɣT I found different result. It is around 48 (1) dyn/cm.
Actually, I expected to have the same values with the two ensembles, but
not.

Am I missing something that is straightforward?

Regards

-- 
Ozge Engin
 ★☆
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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus) as supposed
to the displacement along a given vector component?



For diagnosing weird behavior, I would always start with the primary data, not 
any post-processed interpretation of it.  Use the pullx.xvg file.  Any weird 
changes in sign or sudden changes in magnitude would indicate problems.  If you 
start manipulating the data, you may be hiding the real reason for the problem.


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file


That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
group, then displacement (dX,dY,dZ) of the pull group relative to the
reference.  Not all terms may be present, depending on the axis along
which you're pulling, i.e. if you only pull along Z, there will be two
terms in pullx.xvg - Z and dZ.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Justin

I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them  again in more detail and post
back.


Plotting the pullx.xvg file(s) may be useful, too, to indicate where
any weird jumps or sudden changes in position might occur.  Mapping
that information back onto the trajectory could help focus your
attention.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

O.K thanks anyway


I saw the plots you posted during a conversation with Chris, but I'll
ask the obvious anyway: have you watched the trajectories for any of
the problematic windows?  It didn't seem like you had two metastable
states, but maybe having a look at the movie would shed some light on
what's going on.  I know that's the first thing I'd do.

-Justin


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm,
but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull
code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the
output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start
reference at

t=0
   07236
   172   360   4.290 4.290

why is this so?


grompp always assigns the numerical middle atom of a group as
the
PBC 

...unless over-ridden by providing a different value for
pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] pbc atom

[Gavin Melaugh]

For the umbrella sampling I am not pulling in any direction I am just
applying the umbrella potential so that two molecules can sample space
about a give value of r0 (COM distance). Maybe I am confused but should
I not plot the absolute value of the displacement (modulus) as supposed
to the displacement along a given vector component?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> I always used g_dist to plot the COM distances because the pullx.xvg
>> files doesn't give this value directly. Can you access the COM distance
>> from the pullx.xvg file
>>
>
> That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference
> group, then displacement (dX,dY,dZ) of the pull group relative to the
> reference.  Not all terms may be present, depending on the axis along
> which you're pulling, i.e. if you only pull along Z, there will be two
> terms in pullx.xvg - Z and dZ.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Justin

 I have looked at the movies but it's very hard to tell what's going on
 as I save teh trajectories every 25 steps for every 5000 step
 simulation (100 ns). Ill look at them  again in more detail and post
 back.

>>> Plotting the pullx.xvg file(s) may be useful, too, to indicate where
>>> any weird jumps or sudden changes in position might occur.  Mapping
>>> that information back onto the trajectory could help focus your
>>> attention.
>>>
>>> -Justin
>>>
 Gavin

 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> O.K thanks anyway
>>
> I saw the plots you posted during a conversation with Chris, but I'll
> ask the obvious anyway: have you watched the trajectories for any of
> the problematic windows?  It didn't seem like you had two metastable
> states, but maybe having a look at the movie would shed some light on
> what's going on.  I know that's the first thing I'd do.
>
> -Justin
>
>> Justin A. Lemkul wrote:
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm,
 but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>>> Sorry, no clue.
>>>
>>> -Justin
>>>
 Cheers

 Gavin

 Justin A. Lemkul wrote:
> Justin A. Lemkul wrote:
>> Gavin Melaugh wrote:
>>> Hi all
>>>
>>> I am generating a series of configurations using the pull
>>> code to
>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
>>> output
>>> from grommp gives me info on pbc atom.
>>>
>>> Pull group  natoms  pbc atom  distance at start
>>> reference at
>>> t=0
>>>07236
>>>172   360   4.290 4.290
>>>
>>> why is this so?
>>>
>> grompp always assigns the numerical middle atom of a group as
>> the
>> PBC 
> ...unless over-ridden by providing a different value for
> pbc_pullatom1.
>
> -Justin
>
>> reference point.  In the case of pbc=no, it shouldn't matter.
>>
>> http://manual.gromacs.org/current/online/mdp_opt.html#pull
>>
>> -Justin
>>
>>> Cheers
>>>
>>> Gavin

>>
>>
>

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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file



That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference group, then 
displacement (dX,dY,dZ) of the pull group relative to the reference.  Not all 
terms may be present, depending on the axis along which you're pulling, i.e. if 
you only pull along Z, there will be two terms in pullx.xvg - Z and dZ.


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Justin

I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them  again in more detail and post
back.


Plotting the pullx.xvg file(s) may be useful, too, to indicate where
any weird jumps or sudden changes in position might occur.  Mapping
that information back onto the trajectory could help focus your
attention.

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

O.K thanks anyway


I saw the plots you posted during a conversation with Chris, but I'll
ask the obvious anyway: have you watched the trajectories for any of
the problematic windows?  It didn't seem like you had two metastable
states, but maybe having a look at the movie would shed some light on
what's going on.  I know that's the first thing I'd do.

-Justin


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the
output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at
t=0
   07236
   172   360   4.290 4.290

why is this so?


grompp always assigns the numerical middle atom of a group as the
PBC 

...unless over-ridden by providing a different value for
pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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] pbc atom

[Gavin Melaugh]

I always used g_dist to plot the COM distances because the pullx.xvg
files doesn't give this value directly. Can you access the COM distance
from the pullx.xvg file

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Justin
>>
>> I have looked at the movies but it's very hard to tell what's going on
>> as I save teh trajectories every 25 steps for every 5000 step
>> simulation (100 ns). Ill look at them  again in more detail and post
>> back.
>>
>
> Plotting the pullx.xvg file(s) may be useful, too, to indicate where
> any weird jumps or sudden changes in position might occur.  Mapping
> that information back onto the trajectory could help focus your
> attention.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 O.K thanks anyway

>>> I saw the plots you posted during a conversation with Chris, but I'll
>>> ask the obvious anyway: have you watched the trajectories for any of
>>> the problematic windows?  It didn't seem like you had two metastable
>>> states, but maybe having a look at the movie would shed some light on
>>> what's going on.  I know that's the first thing I'd do.
>>>
>>> -Justin
>>>
 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Thanks Justin
>>
>> Have you any idea why when generating umbrella histograms for the
>> pmf I
>> would get two peaks in the histograms above a distance of 2 nm, but
>> below 2 nm I get well behaved histograms that lead to a very
>> good profile in the pmf. To the best of my knowledge the
>> configurations
>> are all very well equilibrated at their respective COM distances.
>> Umbrella sampling is performed on all windows using a force
>> constant of
>> 1000 kj/mol at 600 K.
>>
> Sorry, no clue.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>> Justin A. Lemkul wrote:
 Gavin Melaugh wrote:
> Hi all
>
> I am generating a series of configurations using the pull code to
> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
> output
> from grommp gives me info on pbc atom.
>
> Pull group  natoms  pbc atom  distance at start reference at
> t=0
>07236
>172   360   4.290 4.290
>
> why is this so?
>
 grompp always assigns the numerical middle atom of a group as the
 PBC 
>>> ...unless over-ridden by providing a different value for
>>> pbc_pullatom1.
>>>
>>> -Justin
>>>
 reference point.  In the case of pbc=no, it shouldn't matter.

 http://manual.gromacs.org/current/online/mdp_opt.html#pull

 -Justin

> Cheers
>
> Gavin

>>
>>
>

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Re: [gmx-users] help with git

[Roland Schulz]

On Tue, Aug 24, 2010 at 9:01 AM, Alan  wrote:

> Ok, doing:
>
> git reset origin/release-4-5-patches
> git checkout origin/release-4-5-patches
>
I'm confused what you are trying to do. But you are not supposed to checkout
a remote branch.

> git pull
> Already up-to-date.
>
> restored the sanity of system.
>
> On 24 August 2010 13:52, Alan  wrote:
>
>> Thanks Carsten, but now nothing is not working, not even what was doing
>> so:
>>
>> git reset --hard
>> HEAD is now at 5e3473a Merge branch 'release-4-5-patches'
>>  amadeus[2216]:~/workspace/gromacs% git checkout release-4-5-patches
>> Already on 'release-4-5-patches'
>> Your branch and 'origin/release-4-5-patches' have diverged,
>> and have 37 and 31 different commit(s) each, respectively.
>> amadeus[2217]:~/workspace/gromacs% git pull
>> Auto-merging include/physics.h
>> Auto-merging include/resall.h
>> CONFLICT (content): Merge conflict in include/resall.h
>> Auto-merging include/string2.h
>> CONFLICT (content): Merge conflict in include/string2.h
>> Auto-merging include/vec.h
>> CONFLICT (content): Merge conflict in include/vec.h
>> Auto-merging src/gmxlib/string2.c
>> Auto-merging src/kernel/gen_vsite.c
>> Auto-merging src/kernel/pdb2gmx.c
>> Auto-merging src/kernel/pdb2top.c
>> CONFLICT (content): Merge conflict in src/kernel/pdb2top.c
>> Auto-merging src/kernel/resall.c
>> Auto-merging src/kernel/ter_db.c
>> Auto-merging src/tools/gmx_membed.c
>> Automatic merge failed; fix conflicts and then commit the result.
>> amadeus[2218]:~/workspace/gromacs%
>>
>>
>>
>> On 24 August 2010 12:10, Carsten Kutzner  wrote:
>>
>>> On Aug 24, 2010, at 12:57 PM, Alan wrote:
>>>
>>> Hi there,
>>>
>>> I want to change from release-4-5-patches to master
>>>
>>> I am trying:
>>>
>>> git reset master
>>> git checkout master
>>>
>>> git pull
>>> error: Your local changes to 'include/resall.h' would be overwritten by
>>> merge.  Aborting.
>>> Please, commit your changes or stash them before you can merge.
>>>
>>> git stash
>>> Saved working directory and index state WIP on master: 5e3473a Merge
>>> branch 'release-4-5-patches'
>>> HEAD is now at 5e3473a Merge branch 'release-4-5-patches'
>>>
>>> But I don't want branch 'release-4-5-patches'!
>>>
>>> Indeed, I am finding git very annoying to use.
>>>
>>> All I wanted in svn lingo is to change to a branch and if there's
>>> conflict, ignore all changes in my side and revert any modification to
>>> what's in the repository.
>>>
>>> git reset --hard
>>> will remove all your modifications to that branch that are not checked in
>>> yet. You might
>>> want to save include/resall.h elsewhere if you still need your
>>> modifications.
>>>
>>> Then
>>> git checkout master
>>>
>>> will check out the master branch. You might need to "git pull" after you
>>> checked
>>> out the master so that you are up-to-date with the gromacs repository.
>>>
>>> Carsten
>>>
>>>
>>> Is it possible with git?
>>>
>>> Thanks,
>>>
>>> Alan
>>>
>>>
>>> --
>>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>>> Department of Biochemistry, University of Cambridge.
>>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>> >>http://www.bio.cam.ac.uk/~awd28<<
>>>  --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>>
>>>
>>>
>>> --
>>> Dr. Carsten Kutzner
>>> Max Planck Institute for Biophysical Chemistry
>>> Theoretical and Computational Biophysics
>>> Am Fassberg 11, 37077 Goettingen, Germany
>>> Tel. +49-551-2012313, Fax: +49-551-2012302
>>> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
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>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>>
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>> >>http://www.bio.cam.ac.uk/~awd28<<
>>
>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-req

Re: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa

[Alan]

Thanks Berk, it seems to be working now.

Alan

On 24 August 2010 08:54, Berk Hess  wrote:

>  Hi,
>
> This was due to two simultaneous issues. I fixed them both for the next
> beta release.
> Note that using HIS iso HISE as a residue name would solve the problem.
> For 4.5 this should be the normal input, since residue names from the pdb
> are now preserved.
>
> Berk
>
> --
> From: alanwil...@gmail.com
> Date: Mon, 23 Aug 2010 17:45:03 +0100
>
> To: gmx-users@gromacs.org
> Subject: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa
>
>
> Hi there,
>
> I have a system with 'HISE' and using gmx 4.5.
>
> ATOM 20  N   HISE2   6.376   3.718  -0.053  1.00  0.00
>   N
> ATOM 21  H   HISE2   5.980   4.646  -0.135  1.00  0.00
>   H
> ATOM 22  CA  HISE2   7.843   3.744  -0.109  1.00  0.00
>   C
> ATOM 23  HA  HISE2   8.260   3.319   0.806  1.00  0.00
>   H
> ATOM 24  CB  HISE2   8.319   2.925  -1.327  1.00  0.00
>   C
> ATOM 25  HB2 HISE2   7.855   1.940  -1.312  1.00  0.00
>   H
> ATOM 26  HB1 HISE2   7.985   3.435  -2.233  1.00  0.00
>   H
> ATOM 27  CG  HISE2   9.807   2.703  -1.450  1.00  0.00
>   C
> ATOM 28  ND1 HISE2  10.461   2.463  -2.655  1.00  0.00
>   N
> ATOM 29  CE1 HISE2  11.770   2.542  -2.382  1.00  0.00
>   C
> ATOM 30  HE1 HISE2  12.557   2.484  -3.124  1.00  0.00
>   H
> ATOM 31  NE2 HISE2  11.969   2.794  -1.078  1.00  0.00
>   N
> ATOM 32  HE2 HISE2  12.817   3.173  -0.672  1.00  0.00
>   H
> ATOM 33  CD2 HISE2  10.740   2.839  -0.459  1.00  0.00
>   C
> ATOM 34  HD2 HISE2  10.579   3.098   0.574  1.00  0.00
>   H
> ATOM 35  C   HISE2   8.279   5.228  -0.214  1.00  0.00
>   C
> ATOM 36  O   HISE2   7.440   6.079  -0.525  1.00  0.00
>   O
>
> when trying:
>
> pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none
>
> Identified residue HISE1 as a starting terminus.
> Identified residue HISE3 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>HISE1   HISE2
>NE214   NE231
>HISE2   NE231   0.854
>HISE3   NE248   0.751   0.847
> Start terminus: NH3+
> End terminus: COO-
>
> ---
> Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39
> Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c,
> line: 583
>
> Fatal error:
> Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms
> while sorting atoms. Maybe different protonation state.
>  Remove this hydrogen or choose a different protonation state.
>  Option -ignh will ignore all hydrogens in the input.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence
> != HISE)
>
> Many thanks in advance,
>
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <<
>
> -- 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/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/mailing_lists/users.php
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

Justin

I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them  again in more detail and post back.



Plotting the pullx.xvg file(s) may be useful, too, to indicate where any weird 
jumps or sudden changes in position might occur.  Mapping that information back 
onto the trajectory could help focus your attention.


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

O.K thanks anyway


I saw the plots you posted during a conversation with Chris, but I'll
ask the obvious anyway: have you watched the trajectories for any of
the problematic windows?  It didn't seem like you had two metastable
states, but maybe having a look at the movie would shed some light on
what's going on.  I know that's the first thing I'd do.

-Justin


Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the
pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the
configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force
constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the
output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at
t=0
   07236
   172   360   4.290 4.290

why is this so?


grompp always assigns the numerical middle atom of a group as the
PBC 

...unless over-ridden by providing a different value for
pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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] pbc atom

[Gavin Melaugh]

Justin

I have looked at the movies but it's very hard to tell what's going on
as I save teh trajectories every 25 steps for every 5000 step
simulation (100 ns). Ill look at them  again in more detail and post back.

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> O.K thanks anyway
>>
>
> I saw the plots you posted during a conversation with Chris, but I'll
> ask the obvious anyway: have you watched the trajectories for any of
> the problematic windows?  It didn't seem like you had two metastable
> states, but maybe having a look at the movie would shed some light on
> what's going on.  I know that's the first thing I'd do.
>
> -Justin
>
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Thanks Justin

 Have you any idea why when generating umbrella histograms for the
 pmf I
 would get two peaks in the histograms above a distance of 2 nm, but
 below 2 nm I get well behaved histograms that lead to a very
 good profile in the pmf. To the best of my knowledge the
 configurations
 are all very well equilibrated at their respective COM distances.
 Umbrella sampling is performed on all windows using a force
 constant of
 1000 kj/mol at 600 K.

>>> Sorry, no clue.
>>>
>>> -Justin
>>>
 Cheers

 Gavin

 Justin A. Lemkul wrote:
> Justin A. Lemkul wrote:
>> Gavin Melaugh wrote:
>>> Hi all
>>>
>>> I am generating a series of configurations using the pull code to
>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the
>>> output
>>> from grommp gives me info on pbc atom.
>>>
>>> Pull group  natoms  pbc atom  distance at start reference at
>>> t=0
>>>07236
>>>172   360   4.290 4.290
>>>
>>> why is this so?
>>>
>> grompp always assigns the numerical middle atom of a group as the
>> PBC 
> ...unless over-ridden by providing a different value for
> pbc_pullatom1.
>
> -Justin
>
>> reference point.  In the case of pbc=no, it shouldn't matter.
>>
>> http://manual.gromacs.org/current/online/mdp_opt.html#pull
>>
>> -Justin
>>
>>> Cheers
>>>
>>> Gavin

>>
>>
>

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Re: [gmx-users] help with git

[Alan]

Ok, doing:

git reset origin/release-4-5-patches
git checkout origin/release-4-5-patches
git pull
Already up-to-date.

restored the sanity of system.

On 24 August 2010 13:52, Alan  wrote:

> Thanks Carsten, but now nothing is not working, not even what was doing so:
>
> git reset --hard
> HEAD is now at 5e3473a Merge branch 'release-4-5-patches'
> amadeus[2216]:~/workspace/gromacs% git checkout release-4-5-patches
> Already on 'release-4-5-patches'
> Your branch and 'origin/release-4-5-patches' have diverged,
> and have 37 and 31 different commit(s) each, respectively.
> amadeus[2217]:~/workspace/gromacs% git pull
> Auto-merging include/physics.h
> Auto-merging include/resall.h
> CONFLICT (content): Merge conflict in include/resall.h
> Auto-merging include/string2.h
> CONFLICT (content): Merge conflict in include/string2.h
> Auto-merging include/vec.h
> CONFLICT (content): Merge conflict in include/vec.h
> Auto-merging src/gmxlib/string2.c
> Auto-merging src/kernel/gen_vsite.c
> Auto-merging src/kernel/pdb2gmx.c
> Auto-merging src/kernel/pdb2top.c
> CONFLICT (content): Merge conflict in src/kernel/pdb2top.c
> Auto-merging src/kernel/resall.c
> Auto-merging src/kernel/ter_db.c
> Auto-merging src/tools/gmx_membed.c
> Automatic merge failed; fix conflicts and then commit the result.
> amadeus[2218]:~/workspace/gromacs%
>
>
>
> On 24 August 2010 12:10, Carsten Kutzner  wrote:
>
>> On Aug 24, 2010, at 12:57 PM, Alan wrote:
>>
>> Hi there,
>>
>> I want to change from release-4-5-patches to master
>>
>> I am trying:
>>
>> git reset master
>> git checkout master
>>
>> git pull
>> error: Your local changes to 'include/resall.h' would be overwritten by
>> merge.  Aborting.
>> Please, commit your changes or stash them before you can merge.
>>
>> git stash
>> Saved working directory and index state WIP on master: 5e3473a Merge
>> branch 'release-4-5-patches'
>> HEAD is now at 5e3473a Merge branch 'release-4-5-patches'
>>
>> But I don't want branch 'release-4-5-patches'!
>>
>> Indeed, I am finding git very annoying to use.
>>
>> All I wanted in svn lingo is to change to a branch and if there's
>> conflict, ignore all changes in my side and revert any modification to
>> what's in the repository.
>>
>> git reset --hard
>> will remove all your modifications to that branch that are not checked in
>> yet. You might
>> want to save include/resall.h elsewhere if you still need your
>> modifications.
>>
>> Then
>> git checkout master
>>
>> will check out the master branch. You might need to "git pull" after you
>> checked
>> out the master so that you are up-to-date with the gromacs repository.
>>
>> Carsten
>>
>>
>> Is it possible with git?
>>
>> Thanks,
>>
>> Alan
>>
>>
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>> >>http://www.bio.cam.ac.uk/~awd28<<
>>  --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>
>>
>>
>> --
>> Dr. Carsten Kutzner
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical and Computational Biophysics
>> Am Fassberg 11, 37077 Goettingen, Germany
>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>>
>>
>>
>>
>>
>> --
>>
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>
>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

O.K thanks anyway



I saw the plots you posted during a conversation with Chris, but I'll ask the 
obvious anyway: have you watched the trajectories for any of the problematic 
windows?  It didn't seem like you had two metastable states, but maybe having a 
look at the movie would shed some light on what's going on.  I know that's the 
first thing I'd do.


-Justin



Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.


Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?

grompp always assigns the numerical middle atom of a group as the PBC 

...unless over-ridden by providing a different value for pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin







--


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] help with git

[Alan]

Thanks Carsten, but now nothing is not working, not even what was doing so:

git reset --hard
HEAD is now at 5e3473a Merge branch 'release-4-5-patches'
amadeus[2216]:~/workspace/gromacs% git checkout release-4-5-patches
Already on 'release-4-5-patches'
Your branch and 'origin/release-4-5-patches' have diverged,
and have 37 and 31 different commit(s) each, respectively.
amadeus[2217]:~/workspace/gromacs% git pull
Auto-merging include/physics.h
Auto-merging include/resall.h
CONFLICT (content): Merge conflict in include/resall.h
Auto-merging include/string2.h
CONFLICT (content): Merge conflict in include/string2.h
Auto-merging include/vec.h
CONFLICT (content): Merge conflict in include/vec.h
Auto-merging src/gmxlib/string2.c
Auto-merging src/kernel/gen_vsite.c
Auto-merging src/kernel/pdb2gmx.c
Auto-merging src/kernel/pdb2top.c
CONFLICT (content): Merge conflict in src/kernel/pdb2top.c
Auto-merging src/kernel/resall.c
Auto-merging src/kernel/ter_db.c
Auto-merging src/tools/gmx_membed.c
Automatic merge failed; fix conflicts and then commit the result.
amadeus[2218]:~/workspace/gromacs%



On 24 August 2010 12:10, Carsten Kutzner  wrote:

> On Aug 24, 2010, at 12:57 PM, Alan wrote:
>
> Hi there,
>
> I want to change from release-4-5-patches to master
>
> I am trying:
>
> git reset master
> git checkout master
>
> git pull
> error: Your local changes to 'include/resall.h' would be overwritten by
> merge.  Aborting.
> Please, commit your changes or stash them before you can merge.
>
> git stash
> Saved working directory and index state WIP on master: 5e3473a Merge branch
> 'release-4-5-patches'
> HEAD is now at 5e3473a Merge branch 'release-4-5-patches'
>
> But I don't want branch 'release-4-5-patches'!
>
> Indeed, I am finding git very annoying to use.
>
> All I wanted in svn lingo is to change to a branch and if there's conflict,
> ignore all changes in my side and revert any modification to what's in the
> repository.
>
> git reset --hard
> will remove all your modifications to that branch that are not checked in
> yet. You might
> want to save include/resall.h elsewhere if you still need your
> modifications.
>
> Then
> git checkout master
>
> will check out the master branch. You might need to "git pull" after you
> checked
> out the master so that you are up-to-date with the gromacs repository.
>
> Carsten
>
>
> Is it possible with git?
>
> Thanks,
>
> Alan
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>  --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] pbc atom

[Gavin Melaugh]

O.K thanks anyway


Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Thanks Justin
>>
>> Have you any idea why when generating umbrella histograms for the pmf I
>> would get two peaks in the histograms above a distance of 2 nm, but
>> below 2 nm I get well behaved histograms that lead to a very
>> good profile in the pmf. To the best of my knowledge the configurations
>> are all very well equilibrated at their respective COM distances.
>> Umbrella sampling is performed on all windows using a force constant of
>> 1000 kj/mol at 600 K.
>>
>
> Sorry, no clue.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Justin A. Lemkul wrote:

 Gavin Melaugh wrote:
> Hi all
>
> I am generating a series of configurations using the pull code to
> calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
> from grommp gives me info on pbc atom.
>
> Pull group  natoms  pbc atom  distance at start reference at t=0
>07236
>172   360   4.290 4.290
>
> why is this so?
>
 grompp always assigns the numerical middle atom of a group as the PBC 
>>> ...unless over-ridden by providing a different value for pbc_pullatom1.
>>>
>>> -Justin
>>>
 reference point.  In the case of pbc=no, it shouldn't matter.

 http://manual.gromacs.org/current/online/mdp_opt.html#pull

 -Justin

> Cheers
>
> Gavin
>>
>>
>

-- 
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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.



Sorry, no clue.

-Justin


Cheers

Gavin

Justin A. Lemkul wrote:


Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?

grompp always assigns the numerical middle atom of a group as the PBC 

...unless over-ridden by providing a different value for pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin





--


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] pbc atom

[Gavin Melaugh]

Thanks Justin

Have you any idea why when generating umbrella histograms for the pmf I
would get two peaks in the histograms above a distance of 2 nm, but
below 2 nm I get well behaved histograms that lead to a very
good profile in the pmf. To the best of my knowledge the configurations
are all very well equilibrated at their respective COM distances.
Umbrella sampling is performed on all windows using a force constant of
1000 kj/mol at 600 K.

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Justin A. Lemkul wrote:
>>
>>
>> Gavin Melaugh wrote:
>>> Hi all
>>>
>>> I am generating a series of configurations using the pull code to
>>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
>>> from grommp gives me info on pbc atom.
>>>
>>> Pull group  natoms  pbc atom  distance at start reference at t=0
>>>07236
>>>172   360   4.290 4.290
>>>
>>> why is this so?
>>>
>>
>> grompp always assigns the numerical middle atom of a group as the PBC 
>
> ...unless over-ridden by providing a different value for pbc_pullatom1.
>
> -Justin
>
>> reference point.  In the case of pbc=no, it shouldn't matter.
>>
>> http://manual.gromacs.org/current/online/mdp_opt.html#pull
>>
>> -Justin
>>
>>> Cheers
>>>
>>> Gavin
>>
>

-- 
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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?



grompp always assigns the numerical middle atom of a group as the PBC 


...unless over-ridden by providing a different value for pbc_pullatom1.

-Justin


reference point.  In the case of pbc=no, it shouldn't matter.

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin




--


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] gmx 4.5 and openmm on Mac, still not compiling

[Rossen Apostolov]

 Hi Alan,

With OpenMM you don't need SSE kernels. If you look at CMakeCache.txt 
you'll see that




Hi there,

I've tried before and the error still basically the same (line error 
in 'nb_kernel400_x86_64_sse.c' was 630, now's 629) .


I am using gmx 4.5 release-4-5-patches branch.

git pull
rm -fr build
mkdir -p build
cd build
cmake -D BUILD_SHARED_LIBS=ON -DGMX_OPENMM=OFF ..

Since GMX_OPENMM=OFF, GMX_ACCELERATION is automatically set to SSE.

make clean

This command doesn't remove CMaceCache.txt!

make -j 2
sudo make install # all fine till here
make clean
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -D BUILD_SHARED_LIBS=OFF -DGMX_OPENMM=ON ..
Now GMX_OPENMM is ON, *but* GMX_ACCELERATION is still SSE (the value is 
read from the cache). This is an issue with the cmake system. You should 
either remove CMakeCache.txt or add an explicit -DGMX_ACCELERATION=OFF 
to the cmake command.


This is a workaround at the moment but the issue should be fixed.

Rossen

make mdrun

[snip]
[ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/version.c.o
[ 56%] Building C object 
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c: 
In function ‘nb_kernel400nf_x86_64_sse’:
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: 
error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function)
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: 
error: (Each undeclared identifier is reported only once
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: 
error: for each function it appears in.)
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: 
error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function)
make[3]: *** 
[src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o] 
Error 1

make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2

Any help would be appreciated.

Thanks,

Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28 <<


--
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Re: [gmx-users] pbc atom

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?



grompp always assigns the numerical middle atom of a group as the PBC reference 
point.  In the case of pbc=no, it shouldn't matter.


http://manual.gromacs.org/current/online/mdp_opt.html#pull

-Justin


Cheers

Gavin


--


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] pbc atom

[Gavin Melaugh]

Hi all

I am generating a series of configurations using the pull code to
calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
from grommp gives me info on pbc atom.

Pull group  natoms  pbc atom  distance at start reference at t=0
   07236
   172   360   4.290 4.290

why is this so?

Cheers

Gavin
-- 
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Re: [gmx-users] GB Parameters

[Per Larsson]

surface tension?
>>> (c.)  pi: ?
>>> (d.)  gbr: generalized born radius?  These values correspond to sigma/2 
>>> from Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657).  
>>> However the generalized born radius is equal to Rvdw plus a dielectric 
>>> offset distance, according to Still et al's 1997 J. Phys. Chem. A paper (v. 
>>> 101, p. 3005).  This would mean the dielectric offset distance is set to 
>>> zero (?).  
>>> (e.)  hct: HCT parameter
>>> 
>>> With an eventual goal of implementing implicit solvent using my lab's force 
>>> field, insight into the meaning of the columns and/or references for their 
>>> origin would be greatly appreciated. 
>>> 
>>> Thanks in advance! 
>>> 
>>> Sincerely yours,
>>> 
>>> E. A. Ploetz
>>> -- 
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>> -- 
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> 
> 
> --
> 
> Message: 2
> Date: Mon, 23 Aug 2010 13:01:45 -0700 (PDT)
> From: "Bruce D. Ray" 
> Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field
>   [Justin]
> To: Discussion list for GROMACS users 
> Message-ID: <508235.43845...@web35802.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> On Mon, August 23, 2010 12:12 PM, Eudes Fileti  wrote:
> 
>> Well, the line 40 is just one of the 36 parameters not found!
>> In this link ( https://sites.google.com/site/fileti/ ) I put
>> the complete files. 
>> I know I need to determine which bond type should be called
>> and I believe that it has been done, but I don't know why
>> it's not being found.
> 
> Well, I'm not Justin, but as I look at your topology, I see
> that you have a bond from atom 3, type CC322, to atom 6,
> also type CC322.  However, when I look at the parameters you
> give in the bondtypes section, I cannot find a CC322  CC322
> bond defined.  Either the entry is missing or you did not
> post a complete set of force field entries.
> 
> Missing entries might be the cause of theother parameters
> not found as well, which is what was suggested to you
> previously.
> 
> 
> -- 
> Bruce D. Ray, Ph.D.
> Associate Scientist
> IUPUI
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN  46202-3273
> 
> 
> 
> 
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> 
> --
> 
> Message: 3
> Date: Mon, 23 Aug 2010 17:46:20 -0300
> From: Eudes Fileti 
> Subject: Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force
>   field [Mark,Justin]
> To: gmx-users@gromacs.org
> Message-ID:
>   
> Content-Type: text/plain; charset="windows-1252"
> 
> Ol�,
> Mark and Justin.
> Solved.
> I did what you suggested and I got all the default values.
> 
> Muito obrigado!
> eef
> 
> ___
> Eudes Eterno Fileti
> Centro de Ci�ncias Naturais e Humanas
> Universidade Federal do ABC � CCNH
> Av. dos Estados, 5001
> Santo Andr� - SP - Brasil
> CEP 09210-971
> +55.11.4996-0196
> http://fileti.ufabc.edu.br
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> --
> 
> Message: 4
> Date: Tue, 24 Aug 2010 13:09:55 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] Does anyone know how to get the file
>   charmm_gromacs.tar.gz?
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: text/plain; charset="us-ascii"
> 
> 
> 
> - Original Message -
> From: fang yu

Re: [gmx-users] LJ potential

[Florian Dommert]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 08/24/2010 02:27 PM, Sai Pooja wrote:
> Hi,
> 
> If there are n types of atoms in protein, how does one specify:
> 1) Different types of LJ non-bonded interactions for different pairs?
> 2) Modified Coloumb(by a pre-multiplier) interactions for different pairs?
> 
> Pooja
> 
> 

Hi,

 this can be defined in the top file. Take a look at the manual
regarding the force field and different function types for the nonbonded
interactions. This will surely help.

/Flo

- -- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658

EMail: domm...@icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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[gmx-users] LJ potential

[Sai Pooja]

Hi,

If there are n types of atoms in protein, how does one specify:
1) Different types of LJ non-bonded interactions for different pairs?
2) Modified Coloumb(by a pre-multiplier) interactions for different pairs?

Pooja

-- 
Quaerendo Invenietis-Seek and you shall discover.
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Re: [gmx-users] help with git

[Carsten Kutzner]

On Aug 24, 2010, at 12:57 PM, Alan wrote:

> Hi there,
> 
> I want to change from release-4-5-patches to master
> 
> I am trying:
> 
> git reset master
> git checkout master
> 
> git pull
> error: Your local changes to 'include/resall.h' would be overwritten by 
> merge.  Aborting.
> Please, commit your changes or stash them before you can merge.
> 
> git stash
> Saved working directory and index state WIP on master: 5e3473a Merge branch 
> 'release-4-5-patches'
> HEAD is now at 5e3473a Merge branch 'release-4-5-patches'
> 
> But I don't want branch 'release-4-5-patches'!
> 
> Indeed, I am finding git very annoying to use.
> 
> All I wanted in svn lingo is to change to a branch and if there's conflict, 
> ignore all changes in my side and revert any modification to what's in the 
> repository.
git reset --hard 
will remove all your modifications to that branch that are not checked in yet. 
You might
want to save include/resall.h elsewhere if you still need your modifications.

Then 
git checkout master

will check out the master branch. You might need to "git pull" after you checked
out the master so that you are up-to-date with the gromacs repository.

Carsten

> 
> Is it possible with git?
> 
> Thanks,
> 
> Alan
> 
> 
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge. 
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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Re: [gmx-users] GB Parameters

[Elizabeth Ploetz]

.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
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--

Message: 2
Date: Mon, 23 Aug 2010 13:01:45 -0700 (PDT)
From: "Bruce D. Ray" 
Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field
[Justin]
To: Discussion list for GROMACS users 
Message-ID: <508235.43845...@web35802.mail.mud.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

On Mon, August 23, 2010 12:12 PM, Eudes Fileti  wrote:

> Well, the line 40 is just one of the 36 parameters not found!
> In this link ( https://sites.google.com/site/fileti/ ) I put
> the complete files. 
> I know I need to determine which bond type should be called
> and I believe that it has been done, but I don't know why
> it's not being found.

Well, I'm not Justin, but as I look at your topology, I see
that you have a bond from atom 3, type CC322, to atom 6,
also type CC322.  However, when I look at the parameters you
give in the bondtypes section, I cannot find a CC322  CC322
bond defined.  Either the entry is missing or you did not
post a complete set of force field entries.

Missing entries might be the cause of theother parameters
not found as well, which is what was suggested to you
previously.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



  
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Message: 3
Date: Mon, 23 Aug 2010 17:46:20 -0300
From: Eudes Fileti 
Subject: Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force
field [Mark,Justin]
To: gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset="windows-1252"

Ol�,
Mark and Justin.
Solved.
I did what you suggested and I got all the default values.

Muito obrigado!
eef

___
Eudes Eterno Fileti
Centro de Ci�ncias Naturais e Humanas
Universidade Federal do ABC � CCNH
Av. dos Estados, 5001
Santo Andr� - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br
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Message: 4
Date: Tue, 24 Aug 2010 13:09:55 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] Does anyone know how to get the file
charmm_gromacs.tar.gz?
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"



- Original Message -
From: fang yuan 
Date: Tuesday, August 24, 2010 4:52
Subject: Re: [gmx-users] Does anyone know how to get the file 
charmm_gromacs.tar.gz?
To: Discussion list for GROMACS users 

> Hi, I have the same problem, I need to implement the general CHARMM 
> forcefield in gromacs, so I need to know how to convert the rtf files into 
> rtp files in gromacs

There's never been an automated tool for that.

Mark

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Message: 5
Date: Tue, 24 Aug 2010 08:49:38 +0100
From: Alan 
Subject: [gmx-users] gmx 4.5 and openmm on Mac, still not compiling
To: Gromacs 
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi there,

I've tried before and the error still basically the same (line error in
'nb_kernel400_x86_64_sse.c' was 630, now's 629) .

I am using gmx 4.5 release-4-5-patches branch.

git pull
rm -fr build
mkdir -p build
cd build
cmake -D BUILD_SHARED_LIBS=ON -DGMX_OPENMM=OFF ..
make clean
make -j 2
sudo make install # all fine till here
make clean
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -D BUILD_SHARED_LIBS=OFF -DGMX_OPENMM=ON ..
make mdrun

[snip]
[ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/version.c.o
[ 56%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o
/Users/alan/Programmes/groma

[gmx-users] help with git

[Alan]

Hi there,

I want to change from release-4-5-patches to master

I am trying:

git reset master
git checkout master

git pull
error: Your local changes to 'include/resall.h' would be overwritten by
merge.  Aborting.
Please, commit your changes or stash them before you can merge.

git stash
Saved working directory and index state WIP on master: 5e3473a Merge branch
'release-4-5-patches'
HEAD is now at 5e3473a Merge branch 'release-4-5-patches'

But I don't want branch 'release-4-5-patches'!

Indeed, I am finding git very annoying to use.

All I wanted in svn lingo is to change to a branch and if there's conflict,
ignore all changes in my side and revert any modification to what's in the
repository.

Is it possible with git?

Thanks,

Alan


-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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RE: [gmx-users] Software inconsistency error: update_coords called for velocity without VV integrator

[Berk Hess]

Hi,

This is something we forgot to update.
I fixed it for the next beta release.
If you can read/use diff's, you can fix it yourself with the diff below.

Berk

--- a/src/tools/gmx_membed.c
+++ b/src/tools/gmx_membed.c
@@ -3121,9 +3121,12 @@ double do_md_membed(FILE *fplog,t_commrec *cr,int 
nfile,const t_filenm fnm[],
 update_pcouple(fplog,step,ir,state,pcoupl_mu,M,wcycle,
 upd,bInitStep);
 
-/* velocity (for VV) */
-update_coords(fplog,step,ir,mdatoms,state,f,fr->bTwinRange && 
bNStList,fr->f_twin,fcd,
-  
ekind,M,wcycle,upd,FALSE,etrtVELOCITY2,cr,nrnb,constr,&top->idef);
+   if (bVV)
+   {
+   /* velocity half-step update */
+   update_coords(fplog,step,ir,mdatoms,state,f,fr->bTwinRange 
&& bNStList,fr->f_twin,fcd,
+ 
ekind,M,wcycle,upd,FALSE,etrtVELOCITY2,cr,nrnb,constr,&top->idef);
+   }
 
 /* Above, initialize just copies ekinh into ekin,
  * it doesn't copy position (for VV),


Date: Tue, 24 Aug 2010 16:41:35 +0800
From: zhongjin1...@yahoo.com.cn
To: gmx-users@gromacs.org
Subject: [gmx-users] Software inconsistency error: update_coords called for 
velocity without VV integrator






Hi ,
 When I use g_membed in GMX4.5.3 Beta 3 to insert a protein into a DMPC 
bilayer,  I came across such an error:
Program g_membed, VERSION 4.5-beta3
Source code file: update.c, line: 1595
Software inconsistency error:
update_coords called for velocity without VV integrator
For more information and tips for troubleshooting, please check the GROMACS

 
g_membed -f gmem.tpr -p 1b8l.top -xyinit 0.5 -xyend 1 -nxy 1000 -ndiff 11 -c 
OK.pdb
 
Reading file gmem.tpr, VERSION 4.5-beta3 (single precision)
Reading file gmem.tpr, VERSION 4.5-beta3 (single precision)
Select a group to embed in the membrane:
Group 0 ( System) has 16956 elements
Group 1 (Protein) has  3708 elements
Group 2 (  Protein-H) has  2904 elements
Group 3 (C-alpha) has   388 elements
Group 4 (   Backbone) has  1164 elements
Group 5 (  MainChain) has  1556 elements
Group 6 (   MainChain+Cb) has  1904 elements
Group 7 (MainChain+H) has  1940 elements
Group 8 (  SideChain) has 
 1768 elements
Group 9 (SideChain-H) has  1348 elements
Group10 (Prot-Masses) has  3708 elements
Group11 (non-Protein) has 13248 elements
Group12 (  Other) has 13248 elements
Group13 (   DMPC) has 13248 elements
Select a group: 1
Selected 1: 'Protein'
Select a group to embed Protein into (e.g. the membrane):
Group 0 ( System) has 16956 elements
Group 1 (Protein) has  3708 elements
Group 2 (  Protein-H) has  2904 elements
Group 3 (C-alpha) has   388 elements
Group 4 (   Backbone) has  1164 elements
Group 5 (  MainChain) has  1556 elements
Group 6 (   MainChain+Cb) has  1904 elements
Group 7 (MainChain+H) has  1940 elements
Group 8 ( 
 SideChain) has  1768 elements
Group 9 (SideChain-H) has  1348 elements
Group10 (Prot-Masses) has  3708 elements
Group11 (non-Protein) has 13248 elements
Group12 (  Other) has 13248 elements
Group13 (   DMPC) has 13248 elements
Select a group: 13
Selected 13: 'DMPC'
The estimated area of the protein in the membrane is 15.930 nm^2
There are 130 lipids in the membrane part that overlaps the protein.
The area per lipid is 0.6809 nm^2.
Maximum number of lipids that will be removed is 46.
Will resize the protein by a factor of 0.500 in the xy plane and 1.000 in the z 
direction.
This resizing will be done with respect to the geometrical center of all 
protein atoms
that span the membrane region, i.e. z between 1.299 and 6.362
Embedding piece 0 with center of geometry: 4.933612 4.933665 3.830500
Will remove 0 Protein_chain_A molecules
Will remove 0 Protein_chain_B molecules
Will remove 0 Protein_chain_C molecules
Will remove 0 Protein_chain_D molecules
Will remove 37 DMPC molecules
Back Off! I just backed up 1b8l.top to ./#1b8l.top.2#
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'God Rules Over Mankind, Animals, Cosmos and Such'
1000 steps,  2.0 ps.
---
Program g_membed, VERSION 4.5-beta3
Source code file: update.c, line: 1595
Software inconsistency error:
update_coords called for velocity without VV integrator
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
"Look at these, my work-strong arms" (P.J. Harvey)
 
How to solve such an problem? Thanks!
 
Z

[gmx-users] Re: mdrun_hole (zhongjin)

[mwolf]

> Message: 3
> Date: Tue, 24 Aug 2010 16:53:04 +0800 (CST)
> From: zhongjin 
> Subject: [gmx-users] mdrun_hole
> To: gmx-users@gromacs.org
> Message-ID: <670113.94113...@web15607.mail.cnb.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>  I want to use mdrun_hole to insert a protein into a bilayer. Where can I
> get it ? Thanks !
> Zhongjin He

You can also use g_membed, which is a tool in the latest gromacs version.

Regards,
Maarten Wolf

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[gmx-users] mdrun_hole

[zhongjin]

Hi,
 I want to use mdrun_hole to insert a protein into a bilayer. Where can I get 
it ? Thanks !
Zhongjin He


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[gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

[Pär Bjelkmar]

Hi,

The script I've used for the CHARMM port might be of use to you, e-mail me 
offlist if interested. It's not the greatest piece of code (in pyhon) and it is 
written to parse version c32b1. My experience is that the force field structure 
alters quite a bit between CHARMM releases. So writing a script for general 
porting of CHARMM ff to GMX is probably quite a task.

Regards,
Pär Bjelkmar

> Message: 3
> Date: Mon, 23 Aug 2010 14:51:30 -0400
> From: fang yuan 
> Subject: Re: [gmx-users] Does anyone know how to get the file
>   charmm_gromacs.tar.gz?
> To: Discussion list for GROMACS users 
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi, I have the same problem, I need to implement the general CHARMM
> forcefield in gromacs, so I need to know how to convert the rtf files into
> rtp files in gromacs
> 


<><><><><><><><><><><><><><><><><><><><><>
Pär Bjelkmar, Ph.D. student 

Stockholm Center for Biomembrane Research (CBR),
Stockholm Bioinformatics Center (SBC),
Department of Biochemistry and Biophysics (DBB),
Stockholm University

Tel:+46-8-16 2746   
Fax: +46-8-15 3679  
E-mail: bjelk...@cbr.su.se  
Home: http://www.dbb.su.se/User:Bjelkmar
<><><><><><><><><><><><><><><><><><><><><>


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[gmx-users] Software inconsistency error: update_coords called for velocity without VV integrator

[zhongjin]

Hi ,
 When I use g_membed in GMX4.5.3 Beta 3 to insert a protein into a DMPC 
bilayer,  I came across such an error:
Program g_membed, VERSION 4.5-beta3
Source code file: update.c, line: 1595
Software inconsistency error:
update_coords called for velocity without VV integrator
For more information and tips for troubleshooting, please check the GROMACS

 
g_membed -f gmem.tpr -p 1b8l.top -xyinit 0.5 -xyend 1 -nxy 1000 -ndiff 11 -c 
OK.pdb
 
Reading file gmem.tpr, VERSION 4.5-beta3 (single precision)
Reading file gmem.tpr, VERSION 4.5-beta3 (single precision)
Select a group to embed in the membrane:
Group 0 ( System) has 16956 elements
Group 1 (    Protein) has  3708 elements
Group 2 (  Protein-H) has  2904 elements
Group 3 (    C-alpha) has   388 elements
Group 4 (   Backbone) has  1164 elements
Group 5 (  MainChain) has  1556 elements
Group 6 (   MainChain+Cb) has  1904 elements
Group 7 (    MainChain+H) has  1940 elements
Group 8 (  SideChain) has  1768 elements
Group 9 (    SideChain-H) has  1348 elements
Group    10 (    Prot-Masses) has  3708 elements
Group    11 (    non-Protein) has 13248 elements
Group    12 (  Other) has 13248 elements
Group    13 (   DMPC) has 13248 elements
Select a group: 1
Selected 1: 'Protein'
Select a group to embed Protein into (e.g. the membrane):
Group 0 ( System) has 16956 elements
Group 1 (    Protein) has  3708 elements
Group 2 (  Protein-H) has  2904 elements
Group 3 (    C-alpha) has   388 elements
Group 4 (   Backbone) has  1164 elements
Group 5 (  MainChain) has  1556 elements
Group 6 (   MainChain+Cb) has  1904 elements
Group 7 (    MainChain+H) has  1940 elements
Group 8 (  SideChain) has  1768 elements
Group 9 (    SideChain-H) has  1348 elements
Group    10 (    Prot-Masses) has  3708 elements
Group    11 (    non-Protein) has 13248 elements
Group    12 (  Other) has 13248 elements
Group    13 (   DMPC) has 13248 elements
Select a group: 13
Selected 13: 'DMPC'
The estimated area of the protein in the membrane is 15.930 nm^2
There are 130 lipids in the membrane part that overlaps the protein.
The area per lipid is 0.6809 nm^2.
Maximum number of lipids that will be removed is 46.
Will resize the protein by a factor of 0.500 in the xy plane and 1.000 in the z 
direction.
This resizing will be done with respect to the geometrical center of all 
protein atoms
that span the membrane region, i.e. z between 1.299 and 6.362
Embedding piece 0 with center of geometry: 4.933612 4.933665 3.830500
Will remove 0 Protein_chain_A molecules
Will remove 0 Protein_chain_B molecules
Will remove 0 Protein_chain_C molecules
Will remove 0 Protein_chain_D molecules
Will remove 37 DMPC molecules
Back Off! I just backed up 1b8l.top to ./#1b8l.top.2#
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'God Rules Over Mankind, Animals, Cosmos and Such'
1000 steps,  2.0 ps.
---
Program g_membed, VERSION 4.5-beta3
Source code file: update.c, line: 1595
Software inconsistency error:
update_coords called for velocity without VV integrator
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
"Look at these, my work-strong arms" (P.J. Harvey)
 
How to solve such an problem? Thanks!
 
Zhongjin He


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[gmx-users] Wrong charge group assinment: pdb2gmx of 4.5 beta3

[Chiba Shuntaro]

Dear gmx-users,

 

New pdb2gmx seems to be strange that

the net charge of the first group (N terminal) is not decimal number.

 

I put LEU-TRP-VAL.pdb (attached file) into pdb2gmx

and chose ffG53a6 for the force field.

 

In the topol.top (attached file) obtained,

the first and second charge groups are as follows:

 

[ atoms ]
;   nrtype  resnr residue  atom cgnr  charge mass  typeB chargeB massB
; residue  33 LEU rtp LEU  q +1.0
 1  NL33  LEUN   1  0.129  14.0067  ; qtot 0.129
 2  H 33  LEU   H1   1  0.248   1.008   ; qtot 0.377
 3  H 33  LEU   H2   1  0.248   1.008   ; qtot 0.625
 4  H 33  LEU   H3   1  0.248   1.008   ; qtot 0.873
 5  CH1   33  LEU   CA   2  0.127  13.019   ; qtot 1
 6  CH2   33  LEU   CB   2  0  14.027   ; qtot 1

 

I am sorry if I misunderstand it.

 

Best regards,

Shuntaro


LWV.pdb
Description: Binary data


topol.top
Description: Binary data
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RE: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa

[Berk Hess]

Hi,

This was due to two simultaneous issues. I fixed them both for the next beta 
release.
Note that using HIS iso HISE as a residue name would solve the problem.
For 4.5 this should be the normal input, since residue names from the pdb are 
now preserved.

Berk

From: alanwil...@gmail.com
Date: Mon, 23 Aug 2010 17:45:03 +0100
To: gmx-users@gromacs.org
Subject: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa

Hi there,
I have a system with 'HISE' and using gmx 4.5.
ATOM 20  N   HISE2   6.376   3.718  -0.053  1.00  0.00   N  
ATOM 21  H   HISE2   5.980   4.646  -0.135  1.00  0.00   H  

ATOM 22  CA  HISE2   7.843   3.744  -0.109  1.00  0.00   C  
ATOM 23  HA  HISE2   8.260   3.319   0.806  1.00  0.00   H  
ATOM 24  CB  HISE2   8.319   2.925  -1.327  1.00  0.00   C  

ATOM 25  HB2 HISE2   7.855   1.940  -1.312  1.00  0.00   H  
ATOM 26  HB1 HISE2   7.985   3.435  -2.233  1.00  0.00   H  
ATOM 27  CG  HISE2   9.807   2.703  -1.450  1.00  0.00   C  

ATOM 28  ND1 HISE2  10.461   2.463  -2.655  1.00  0.00   N  
ATOM 29  CE1 HISE2  11.770   2.542  -2.382  1.00  0.00   C  
ATOM 30  HE1 HISE2  12.557   2.484  -3.124  1.00  0.00   H  

ATOM 31  NE2 HISE2  11.969   2.794  -1.078  1.00  0.00   N  
ATOM 32  HE2 HISE2  12.817   3.173  -0.672  1.00  0.00   H  
ATOM 33  CD2 HISE2  10.740   2.839  -0.459  1.00  0.00   C  

ATOM 34  HD2 HISE2  10.579   3.098   0.574  1.00  0.00   H  
ATOM 35  C   HISE2   8.279   5.228  -0.214  1.00  0.00   C  
ATOM 36  O   HISE2   7.440   6.079  -0.525  1.00  0.00   O  


when trying:
pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none
Identified residue HISE1 as a starting terminus.

Identified residue HISE3 as a ending terminus.8 out of 8 lines of specbond.dat 
converted successfullySpecial Atom Distance matrix:   HISE1   
HISE2   NE214   NE231

   HISE2   NE231   0.854   HISE3   NE248   0.751   0.847Start terminus: NH3+End 
terminus: COO-
---

Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39Source code file: 
/Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line: 583
Fatal error:Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms

while sorting atoms. Maybe different protonation state. Remove this 
hydrogen or choose a different protonation state. Option -ignh will 
ignore all hydrogens in the input.

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


Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence != 
HISE)
Many thanks in advance,
Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate


Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<



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[gmx-users] gmx 4.5 and openmm on Mac, still not compiling

[Alan]

Hi there,

I've tried before and the error still basically the same (line error in
'nb_kernel400_x86_64_sse.c' was 630, now's 629) .

I am using gmx 4.5 release-4-5-patches branch.

git pull
rm -fr build
mkdir -p build
cd build
cmake -D BUILD_SHARED_LIBS=ON -DGMX_OPENMM=OFF ..
make clean
make -j 2
sudo make install # all fine till here
make clean
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -D BUILD_SHARED_LIBS=OFF -DGMX_OPENMM=ON ..
make mdrun

[snip]
[ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/version.c.o
[ 56%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:
In function ‘nb_kernel400nf_x86_64_sse’:
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function)
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
error: (Each undeclared identifier is reported only once
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
error: for each function it appears in.)
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function)
make[3]: ***
[src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o]
Error 1
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2

Any help would be appreciated.

Thanks,

Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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