[gmx-users] g_hbond segmentation fault

[Yao Yao]

I tried without -dt or -e, still the same problem exists in either case.
Thanks,
Yao

--- On Wed, 9/29/10, David van der Spoel  wrote:

From: David van der Spoel 
Subject: Re: [gmx-users] g_hbond segmentation fault
To: "Discussion list for GROMACS users" 
Date: Wednesday, September 29, 2010, 6:11 AM

On 2010-09-29 08.02, Yao Yao wrote:
> Hi Gmxers,
>
> I used the command line,
>
> g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1
>
> and I got the message like,
>
try without the -dt 1

> --
> Found 1048 different hydrogen bonds in trajectory
> Found 2292 different atom-pairs within hydrogen bonding distance
> Merging hbonds with Acceptor and Donor swapped
> 2/10915 *Segmentation fault*
> __
>
> Anyone knows what could be the reason for this Segmentation Fault ?
>
> A couple of Q's I am also curious,
>
> why do we need to swap Acceptors and Acceptors when merging hbonds?
>
> Does gromacs suggest that the number of different hydrogen bonds in
> trajectory
> should be the same as that of different atom-pairs within hydrogen
> bonding distance?
>
> Thanks,
>
> Yao
>
>
>


-- 
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
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Re: [gmx-users] g_hbond segmentation fault

[David van der Spoel]

On 2010-09-29 08.02, Yao Yao wrote:

Hi Gmxers,

I used the command line,

g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1

and I got the message like,


try without the -dt 1


--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915 *Segmentation fault*
__

Anyone knows what could be the reason for this Segmentation Fault ?

A couple of Q's I am also curious,

why do we need to swap Acceptors and Acceptors when merging hbonds?

Does gromacs suggest that the number of different hydrogen bonds in
trajectory
should be the same as that of different atom-pairs within hydrogen
bonding distance?

Thanks,

Yao






--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] g_hbond segmentation fault

[Yao Yao]

Hi Gmxers,
I used the command line, 
g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1
and I got the message like,
--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915 Segmentation fault
__

Anyone knows what could be the reason for this Segmentation Fault ?
A couple of Q's I am also curious, 
why do we need to swap Acceptors and Acceptors when merging hbonds?
Does gromacs suggest that the number of different hydrogen bonds in 
trajectoryshould be the same as that of different atom-pairs within hydrogen 
bonding distance?
Thanks,
Yao 




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Re: [gmx-users] about pull_init and pull_start

[Justin A. Lemkul]

zhongjin wrote:

Hi all, I am sorry to ask such a question,may it seems very stupid, but I am
very confused about it. pull_init is the reference distance at t=0. the
reference distance is the distance between the pull group and the reference
group? This is a single value, except for geometry position which uses a


Yes.


vector.If it is a single value,it can be negative or positive? pull_start =


By definition, a distance (a scalar quantity) must be positive.


yes,add the COM distance of the starting conformation to pull_init. What it
means? I have seen from somewhere else :Setting pull_start = yes means that
the initial COM distance is the reference distance, and we do not have to
define a reference (pull_init1) separately for each configuration. How is the


Correct.  It's an easy way out.  Using "pull_start = yes" + "pull_init1 = 0" 
means that the initial COM distance (whatever it is) is the reference distance. 
 The equivalent could be accomplished by using "pull_start = no" + "pull_init1 
= (COM distance)"



pulling force caculated? My case may be a little special, I want to use pull=


Hooke's Law.


umbrella,pull_geometry = distance ,but my pull group is very close to
reference group ,the Z coordinate of COM of reference group is 1.81939,1.822
for COM of pull group. I came across a problem :Pull reference distance for
group 1 is negative (-0.20)



You've answered your own question from above without even asking it on the list. 
 You're getting a negative distance, and hence an error.  I don't know what 
settings you're using, but "pull_start = yes" + "pull_init1 = 0" should (in 
theory) solve the issue.


-Justin


Zhongjin He





--


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] about pull_init and pull_start

[zhongjin]

Hi all,
  I am sorry to ask such a question,may it seems very stupid, but I am very 
confused about it.
  pull_init is the reference distance at t=0. the reference distance is the 
distance between the pull group and the reference group? This is a single 
value, except for geometry position which uses a vector.If it is a single 
value,it can be negative or positive?
  pull_start = yes,add the COM distance of the starting conformation to 
pull_init. What it means? I have seen from somewhere else :Setting pull_start = 
yes means that the initial COM distance is the reference distance, and we do 
not have to define a reference (pull_init1) separately for each configuration.
  How is the pulling force caculated?
  My case may be a little special, I want to use pull= umbrella,pull_geometry = 
distance ,but my pull group is very close to reference group ,the Z coordinate 
of COM of reference group is 1.81939,1.822 for COM of pull group. I came across 
a problem :Pull reference distance for group 1 is negative (-0.20)

Zhongjin He



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[gmx-users] topolbuild cannot open logfile

[andrew_m_norris]

Hello i am very new to molecular mechanics so please excuse me if my questions 
are a little naive or stupid.I am trying to minimise a mol2 file with 
topolbuild1_3 using the following command line arguments from within the 
topolbuild directory:
 ./topolbuild  -dir /usr/local/gromacs/share/gromacs/top -ff oplsaa 
-n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move
I get the following error: Fatal error.Source code file: topolbuild.c, line: 
345Cannot open log file zinc_12404782.log
I realise that i will have to go over the parameters again but i was hoping for 
some sort of output. Does anyone know if it is a problem with the parameters of 
the input file shown below or some problem with the way in which topolbuild is 
called ? I am a little unsure how to point to the oplsaa force fields? 
Thanks Andrew
mol2 file:
@MOLECULEZINC12404782   36    38     0     0     
0SMALLUSER_CHARGES[(3R)-1-(1-naphthyl)pyrrolidin-3-yl]methanamine@ATOM  
    1 C1          4.9121    5.4361   -0.0609 C.ar      1 <0>        -0.1104     
 2 C2          3.7311    6.1754   -0.0451 C.ar      1 <0>        -0.1149      3 
C3          2.5180    5.5573   -0.0225 C.ar      1 <0>        -0.1069      4 C4 
         2.4527    4.1553   -0.0151 C.ar      1 <0>        -0.0508      5 C5    
      3.6528    3.4026   -0.0311 C.ar      1 <0>        -0.0373      6 C6       
   4.8869    4.0753   -0.0543 C.ar      1 <0>        -0.1044      7 C7          
3.5890    1.9989   -0.0232 C.ar      1 <0>        -0.1128      8 C8          
2.3798    1.3731   -0.0007 C.ar      1 <0>        -0.0985      9 C9          
1.1942  
  2.1013    0.0157 C.ar      1 <0>        -0.1624     10 C10         1.2135    
3.4800    0.0087 C.ar      1 <0>         0.0930     11 N1          0.0208    
4.1998    0.0243 N.pl3     1 <0>        -0.4642     12 C11        -1.1513    
3.2890   -0.0264 C.3       1 <0>         0.0276     13 C12        -2.3059    
4.1663    0.5194 C.3       1 <0>        -0.1388     14 C13        -1.6180    
4.9899    1.6322 C.3       1 <0>        -0.1313     15 H1         -1.7859    
4.5266    2.6045 H         1 <0>         0.1043     16 C14        -0.1188    
4.9670    1.2811 C.3       1 <0>         0.0431     17 C15        -2.1414    
6.4276    1.6324 C.3       1 <0>         0.0042     18 H2          5.8616    
5.9505   -0.0790 H         1 <0>         0.1273     19 H3          3.7785    
7.2544  
 -0.0504 H         1 <0>         0.1244     20 H4          1.6108    6.1430   
-0.0060 H         1 <0>         0.1264     21 H5          5.8102    3.5153   
-0.0664 H         1 <0>         0.1319     22 H6          4.4986    1.4167   
-0.0357 H         1 <0>         0.1310     23 H7          2.3403    0.2939    
0.0049 H         1 <0>         0.1276     24 H8          0.2481    1.5807    
0.0339 H         1 <0>         0.1299     25 H9         -1.3545    2.9801   
-1.0518 H         1 <0>         0.1004     26 H10        -0.9921    2.4211    
0.6135 H         1 <0>         0.0709     27 H11        -3.0996    3.5449    
0.9341 H         1 <0>         0.0885     28 H12        -2.6948    4.8209   
-0.2606 H         1 <0>         0.0875     29 H13         0.4419    4.4789    
2.0783
 H         1 <0>         0.0705     30 H14         0.2477    5.9836    1.1382 H 
        1 <0>         0.0961     31 H15        -1.5362    7.0345    2.3058 H    
     1 <0>         0.1357     32 H16        -2.0827    6.8358    0.6235 H       
  1 <0>         0.1409     33 H17        -3.9079    7.3788    2.0939 H         
1 <0>         0.4420     34 H18        -4.1089    5.8327    1.5151 H         1 
<0>         0.4364     35 N2         -3.5360    6.4306    2.1084 N.4       1 
<0>        -0.6468     36 H19        -3.5649    6.0740    3.0708 H         1 
<0>         0.4397@BOND     1    1    6 ar     2    1    2 ar     3    
1   18 1     4    2    3 ar     5    2   19 1     6    3    4 ar     7    3   
20 1     8    4   10 ar     9    4    5 ar    10    5
    6 ar    11    5    7 ar    12    6   21 1    13    7    8 ar    14    7   
22 1    15    8    9 ar    16    8   23 1    17    9   10 ar    18    9   24 
1    19   10   11 1    20   11   16 1    21   11   12 1    22   12   13 1    23 
  12   25 1    24   12   26 1    25   13   14 1    26   13   27 1    27   13   
28 1    28   14   15 1    29   14   16 1    30   14   17 1    31   16   29 1    
32   16   30 1    33   17   31 1    34   17   32 1    35   17   35 1    36   33 
  35 1    37   34   35 1    38   35   36 1@





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Re: [gmx-users] Fw: g_hbond segmentation fault

[Yao Yao]

Hi Erik,

Sorry about that, I did not notice it.
I used the command line,
g_hbond -f test.trr -s test.tpr -ac test.xvg -e 100 -dt 1

Thanks,

Yao


--- On Tue, 9/28/10, Erik Marklund  wrote:

> From: Erik Marklund 
> Subject: Re: [gmx-users] Fw: g_hbond segmentation fault
> To: "Discussion list for GROMACS users" 
> Date: Tuesday, September 28, 2010, 6:22 PM
> 
> 
>   
> 
> 
> 
>   
>   
> Yao Yao skrev 2010-09-28 19.25:
> 
>   
> 
>   
> 
> 
>   
> 
>   
> 
> 
> 
> --
> 
>   Found 1048 different hydrogen bonds in
> trajectory
> 
>   Found 2292 different atom-pairs within
> hydrogen
>   bonding distance
> 
>   Merging hbonds with Acceptor and Donor
> swapped
> 
>   2/10915Segmentation fault
> 
>   __
> 
>   
> 
>   Hi guys,
> 
>   
> 
>   I got the msg like above when I ran
> g_hbond in version
>   4.5.
> 
>   Any guess on the problem?
> 
>   
> 
>   Thanks,
> 
>   
> 
>   Yao
> 
>   
> 
>   
> 
>         
> 
> 
>   
> 
>   
> 
>   
>   
> 
> 
> And I replied and asked you what was the command line.
> 
> 
> 
> -- 
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.se
>http://folding.bmc.uu.se/
> 
>   
> 
> 
> -Inline Attachment Follows-
> 
> -- 
> gmx-users mailing list    gmx-users@gromacs.org
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Re: [gmx-users] Fw: g_hbond segmentation fault

[Erik Marklund]

 Yao Yao skrev 2010-09-28 19.25:





--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915Segmentation fault
__

Hi guys,

I got the msg like above when I ran g_hbond in version 4.5.
Any guess on the problem?

Thanks,

Yao





And I replied and asked you what was the command line.

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

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[gmx-users] Fw: g_hbond segmentation fault

[Yao Yao]

--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915Segmentation fault
__

Hi guys,

I got the msg like above when I ran g_hbond in version 4.5.
Any guess on the problem?

Thanks,

Yao


      



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Re: [gmx-users] compiling gromacs4.5 with gpu

[BIN ZHANG]

Dear Roland:

Thanks a lot for your reply.
Also, it seems to me that copying all the libraries from their respect  
folder manually to a common place also works.


Best,
Bin




Hi,

yes that is a bug with cmake (see http://bugzilla.gromacs.org/show_bug.cgi?id=549) 
.
You can either disable BUILD_SHARED_LIBS and or you can ran "make  
install" as a workaround until the bug is fixed.


Roland

On Tue, Sep 28, 2010 at 3:02 AM, BIN ZHANG  wrote:
Hi, there:

I was trying to compile gromacs4.5.1 on a GPU cluster (https://secure.nersc.gov/nusers/systems/dirac/ 
).


The compilation seems to work fine, but in the installation folder,  
only "bin/mdrun-gpu" presents. Is it supposed to be so?


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Re: [gmx-users] Another error that keeps comming up.

[TJ Mustard]

  

  
Found that if I set the setting of "-dlb no" when running the mdrun it would not fail. How could dynamic load balancing do this?

 

TJ Mustard

 


  
   On September 28, 2010 at 3:21 AM TJ Mustard  wrote:
  

  
Hey all,

 

Here is another error that I keep getting. I am trying to "speed up" my md runs with -heavyh and longer time steps. I don't get LINCS errors but I do get this...

 

 

 

Back Off! I just backed up prlog.log to ./#prlog.log.1#
 Getting Loaded...
 Reading file monomer_pr.tpr, VERSION 4.5.1 (single precision)
 Starting 2 threads
 Loaded with Money

 Making 1D domain decomposition 2 x 1 x 1

 Back Off! I just backed up pr.edr to ./#pr.edr.1#
 starting mdrun 'Protein in water'
 25000 steps,    100.0 ps.
 step 900, will finish Mon Sep 27 18:19:07 2010imb F 18%
 NOTE: Turning on dynamic load balancing

 step 1600, will finish Mon Sep 27 18:18:42 2010vol 0.92  imb F  1%
 A list of missing interactions:
     LJC Pairs NB of    278 missing  1
   exclusions of   6966 missing  1

 ---
 Program g4.5.1-mdrun, VERSION 4.5.1
 Source code file: domdec_top.c, line: 173

 Software inconsistency error:
 Some interactions seem to be assigned multiple times
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---

 

 

Some settings:

 

define   = -DPOSRES

dt   = 0.004
 nsteps   = 25000

 

 

; OPTIONS FOR ELECTROSTATICS AND VDW
 ; Method for doing electrostatics
 coulombtype  = PME  ; = Cutoff
 rcoulomb-switch  = 0    ; = 0
 rcoulomb = 0.9  ; = 1
 ; Relative dielectric constant for the medium and the reaction field
 epsilon_r    = 1    ; = 1
 epsilon_rf   = 1    ; = 1
 ; Method for doing Van der Waals
 vdw-type = Cut-off  ; = Cut-off
 ; cut-off lengths  
 rvdw-switch  = 0    ; = 0
 rvdw = 1    ; = 1
 ; Apply long range dispersion corrections for Energy and Pressure
 DispCorr = No   ; = No
 ; Extension of the potential lookup tables beyond the cut-off
 table-extension  = 1    ; = 1
 ; Seperate tables between energy group pairs
 energygrp_table  =  ; =
 ; Spacing for the PME/PPPM FFT grid
 fourierspacing   = 0.12 ; = 0.12
 ; FFT grid size, when a value is 0 fourierspacing will be used
 fourier_nx   = 0    ; = 0
 fourier_ny   = 0    ; = 0
 fourier_nz   = 0    ; = 0
 ; EWALD/PME/PPPM parameters
 pme_order    = 6    ; = 4
 ewald_rtol   = 1e-05    ; = 1e-05
 ewald_geometry   = 3d   ; = 3d
 epsilon_surface  = 0    ; = 0
 optimize_fft = yes  ; = no

 

 

; OPTIONS FOR WEAK COUPLING ALGORITHMS
 ; Temperature coupling 
 tcoupl   = v-rescale    ; = No
 nsttcouple   = -1   ; = -1
 nh-chain-length  = 10   ; = 10
 ; Groups to couple separately
 tc-grps  = RNA SOL  ; =
 ; Time constant (ps) and reference temperature (K)
 tau-t    = 0.1 0.1  ; =
 ref-t    = 300 300  ; =
 ; Pressure coupling
 Pcoupl   = Parrinello-Rahman    ; = No
 Pcoupltype   = Isotropic
 nstpcouple   = -1   ; = -1
 ; Time constant (ps), compressibility (1/bar) and reference P (bar)
 tau-p    = 1    ; = 1
 compressibility  = 4.5e-5   ; =
 ref-p    = 1.0  ; =
 ; Scaling of reference coordinates, No, All or COM
 refcoord_scaling = No   ; = No
 ; Random seed for Andersen thermostat
 andersen_seed    = 815131   ; = 815131

 

 

gen-vel  = yes  ; = no
 gen-temp = 300  ; = 300
 gen-seed = 173529   ; = 173529

 

 

constraints  = all-bonds

 

Any help would be appreciated. It also seems to be in

[gmx-users] Re: MPI and dual-core laptop

[simon sham]

Hi,
I was finally able to get my MPI GROMACS running on my laptop. Thanks for all 
those who have provided invaluable suggestions. 
 
Best,
 
Simon Sham 

--- On Mon, 9/27/10, simon sham  wrote:


From: simon sham 
Subject: MPI and dual-core laptop
To: gmx-users@gromacs.org
Date: Monday, September 27, 2010, 11:42 AM






Hi,
I wanted to test the GROMACS MPI version in my dual-processors laptop. I have 
installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 
4.5.1 with --enable-mpi option, I got the following configuration problem:

"checking whether the MPI cc command works... configure: error: Cannot compile 
and link MPI code with mpicc"


mpicc is in my /usr/local/bin directory.

Questions:
1. Can I run GROMACS 4.5.1 in a dual-processor laptop?
2. If yes, how should I configure the software?

Thanks in advance for your insight.

Best,

Simon Sham




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[gmx-users] Looking for force field for metal oxides

[Sanku M]

Dear gromacs users,
  I was planning to study the interaction of a peptide with a zinc 
oxide ( ZnO) surface.  So, I was  wondering whether there is any forcefield for 
metal oxide especially for Zinc Oxide ( ZnO) in literarure that you can suggest 
that can be used in combination with peptide force-field.
Thanks
Sanku 


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Re: [gmx-users] Grompp Error : Segmentation fault

[Justin A. Lemkul]

Roland Schulz wrote:
Please make sure that the error exists in the latest version. Either 
4.5.1 or if you know how please check the latest GIT version 
from release-4-5-patches. If you still get the error with the latest 
version, please file a bugzilla report and attach all required files.




My first guess would be that these lines are problematic:

; Include TFO topology
#include TFO_amber99.itp

The .itp filename should be enclosed in quotes.

-Justin

On Tue, Sep 28, 2010 at 9:01 AM, Alep Latep > wrote:


Dear Gromacs Users and Developers,

I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my
ionic liquid MD simulation using amber 99 force field. I got my
topology from topolbuild v 1.3. I successfully minimized both cation
and anion separately using cg and steep. Then I include the anion in
the cation system using genbox. I got error from grompp like this: 
--

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Segmentation fault (core dumped)
[a...@neox MD1]$ 
-

Still cant find my answer in the mailing list. Sorry for the large
post, but here's my .mdp and .top


-
title = Conjugated-Gradients Energy Minimization

; Preprocessing
cpp = /lib/cpp
include = -I../top

; Parameters
integrator = cg
emtol = 1.0
nsteps = 5000
nstenergy = 100
nstxtcout = 100
xtc_grps = System
energygrps = System

; Neighboursearching
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
constraints = none
pbc = xyz

-
; Topology from .mol2 file
; topolbuild version 1.3
; Command line:
; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
;
; The force field files to be included
#include "amber99.ff/forcefield.itp"

 [ moleculetype ]
; name  nrexcl
BMIM   3

 [ atoms ]
;  nrtype   resnr   residu   atom   cgnrcharge  mass
1  CT 1  BMIM   C1  -0.17243  12.01100  
;  -0.1724300
2  HC 1  BMIM   H1   0.07139   1.00800  
;  -0.1010400
3  HC 1  BMIM   H1   0.05434   1.00800  
;  -0.0467000
4  HC 1  BMIM   H1   0.05138   1.00800  
;   0.0046800
5  CT 1  BMIM   C2   0.02353  12.01100  
;   0.0282100
6  HC 1  BMIM   H2   0.02417   1.00800  
;   0.0523800
7  HC 1  BMIM   H2   0.02427   1.00800  
;   0.0766500
8  CT 1  BMIM   C3   0.01014  12.01100  
;   0.0867900
9  HC 1  BMIM   H3   0.03312   1.00800  
;   0.1199100
   10  HC 1  BMIM   H3   0.02952   1.00800  
;   0.1494300
   11  NA 1  BMIM   N4   0.05435  14.00670  
;   0.2037800
   12  CC 1  BMIM   C4  -0.17380  12.01100  
;   0.0299800
   13  H4 1  BMIM   H4   0.23709   1.00800  
;   0.2670700
   14  NA 1  BMIM   N6   0.07275  14.00670  
;   0.3398200
   15  CT 1  BMIM   C5  -0.07367  12.01100  
;   0.2661500
   16  H1 1  BMIM   H5   0.10657   1.00800  
;   0.3727200
   17  H1 1  BMIM   H5   0.09108   1.00800  
;   0.4638000
   18  CC 1  BMIM   C6  -0.08433  12.01100  
;   0.3794700
   19  H4 1  BMIM   H6   0.20500   1.00800  
;   0.5844700
   20  CR 1  BMIM   C7  -0.02624  12.01100  
;   0.5582300
   21  H5 1  BMIM   H7   0.21862   1.00800  
;   0.7768500
   22  CT 1  BMIM   C8  -0.18403  12.01100  
;   0.5928200
   23  H1 1  BMIM   H8   0.13823   1.00800  
;   0.7310500
   24  H1 1  BMIM   H8   0.13886   1.00800  
;   0.8699100
   25  H1 1  BMIM   H8   0.13010   1.00800  
;   1.100

; total molecu

Re: [gmx-users] Grompp Error : Segmentation fault

[Roland Schulz]

Please make sure that the error exists in the latest version. Either 4.5.1
or if you know how please check the latest GIT version
from release-4-5-patches. If you still get the error with the latest
version, please file a bugzilla report and attach all required files.

On Tue, Sep 28, 2010 at 9:01 AM, Alep Latep wrote:

> Dear Gromacs Users and Developers,
>
> I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic
> liquid MD simulation using amber 99 force field. I got my topology from
> topolbuild v 1.3. I successfully minimized both cation and anion separately
> using cg and steep. Then I include the anion in the cation system using
> genbox. I got error from grompp like this:
>
> --
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> processing topology...
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Segmentation fault (core dumped)
> [a...@neox MD1]$
>
> -
> Still cant find my answer in the mailing list. Sorry for the large post,
> but here's my .mdp and .top
>
>
> -
> title = Conjugated-Gradients Energy Minimization
>
> ; Preprocessing
> cpp = /lib/cpp
> include = -I../top
>
> ; Parameters
> integrator = cg
> emtol = 1.0
> nsteps = 5000
> nstenergy = 100
> nstxtcout = 100
> xtc_grps = System
> energygrps = System
>
> ; Neighboursearching
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> constraints = none
> pbc = xyz
>
> -
> ; Topology from .mol2 file
> ; topolbuild version 1.3
> ; Command line:
> ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
> ;
> ; The force field files to be included
> #include "amber99.ff/forcefield.itp"
>
>  [ moleculetype ]
> ; name  nrexcl
> BMIM   3
>
>  [ atoms ]
> ;  nrtype   resnr   residu   atom   cgnrcharge  mass
> 1  CT 1  BMIM   C1  -0.17243  12.01100   ;
>  -0.1724300
> 2  HC 1  BMIM   H1   0.07139   1.00800   ;
>  -0.1010400
> 3  HC 1  BMIM   H1   0.05434   1.00800   ;
>  -0.0467000
> 4  HC 1  BMIM   H1   0.05138   1.00800   ;
>   0.0046800
> 5  CT 1  BMIM   C2   0.02353  12.01100   ;
>   0.0282100
> 6  HC 1  BMIM   H2   0.02417   1.00800   ;
>   0.0523800
> 7  HC 1  BMIM   H2   0.02427   1.00800   ;
>   0.0766500
> 8  CT 1  BMIM   C3   0.01014  12.01100   ;
>   0.0867900
> 9  HC 1  BMIM   H3   0.03312   1.00800   ;
>   0.1199100
>10  HC 1  BMIM   H3   0.02952   1.00800   ;
>   0.1494300
>11  NA 1  BMIM   N4   0.05435  14.00670   ;
>   0.2037800
>12  CC 1  BMIM   C4  -0.17380  12.01100   ;
>   0.0299800
>13  H4 1  BMIM   H4   0.23709   1.00800   ;
>   0.2670700
>14  NA 1  BMIM   N6   0.07275  14.00670   ;
>   0.3398200
>15  CT 1  BMIM   C5  -0.07367  12.01100   ;
>   0.2661500
>16  H1 1  BMIM   H5   0.10657   1.00800   ;
>   0.3727200
>17  H1 1  BMIM   H5   0.09108   1.00800   ;
>   0.4638000
>18  CC 1  BMIM   C6  -0.08433  12.01100   ;
>   0.3794700
>19  H4 1  BMIM   H6   0.20500   1.00800   ;
>   0.5844700
>20  CR 1  BMIM   C7  -0.02624  12.01100   ;
>   0.5582300
>21  H5 1  BMIM   H7   0.21862   1.00800   ;
>   0.7768500
>22  CT 1  BMIM   C8  -0.18403  12.01100   ;
>   0.5928200
>23  H1 1  BMIM   H8   0.13823   1.00800   ;
>   0.7310500
>24  H1 1  BMIM   H8   0.13886   1.00800   ;
>   0.8699100
>25  H1 1  BMIM   H8   0.13010   1.00800   ;
>   1.100
> ; total molecule charge =   1.100
>
>  [ bonds ]
> ;   ai  aj   funct  b0  kb
>1 5   1 0.15260  259408.   ; C- C
>1 2   1 0.10900  284512.   ; C- H
>1 3   1 0.10900  284512.   ; C- H
>1 4   1 0.10900  284512.   ; C- H
>5 8   1 0.15260  259408.   ; C- C
>5 6 

Re: [gmx-users] compiling gromacs4.5 with gpu

[Roland Schulz]

Hi,

yes that is a bug with cmake (see
http://bugzilla.gromacs.org/show_bug.cgi?id=549).
You can either disable BUILD_SHARED_LIBS and or you can ran "make install"
as a workaround until the bug is fixed.

Roland

On Tue, Sep 28, 2010 at 3:02 AM, BIN ZHANG  wrote:

> Hi, there:
>
> I was trying to compile gromacs4.5.1 on a GPU cluster (
> https://secure.nersc.gov/nusers/systems/dirac/).
>
> The compilation seems to work fine, but in the installation folder, only
> "bin/mdrun-gpu" presents. Is it supposed to be so?
>
> When I type "./mdrun-gpu -h", the following error occurs:
> ./mdrun-gpu: error while loading shared libraries: libgmxpreprocess.so.6:
> cannot open shared object file: No such file or directory
>
> Do you have any idea what this means?
>
> Thanks a lot,
> Bin
>
> =
> Here are steps I did for compiling:
> export OPENMM_ROOT_DIR=/global/homes/b/bingo/Program/OpenMM2.0-Linux64
> cmake -DGMX_OPENMM=ON
> -DCMAKE_INSTALL_PREFIX=/global/homes/b/bingo/Program/gromacs_gpu
> make mdrun
> make install-mdrun
>
> ==
> Here are the outputs from the cmake
>
> -- The C compiler identification is GNU
> -- The CXX compiler identification is GNU
> -- Check for working C compiler: /usr/bin/gcc
> -- Check for working C compiler: /usr/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs'
> or 'svn'. CTest update will not work.
> -- Performing Test CFLAGS_WARN
> -- Performing Test CFLAGS_WARN - Success
> -- Performing Test CFLAGS_EXCESS_PREC
> -- Performing Test CFLAGS_EXCESS_PREC - Failed
> -- Performing Test CFLAGS_COPT
> -- Performing Test CFLAGS_COPT - Success
> -- Performing Test CFLAGS_NOINLINE
> -- Performing Test CFLAGS_NOINLINE - Success
> -- Performing Test CXXFLAGS_WARN
> -- Performing Test CXXFLAGS_WARN - Success
> -- Performing Test CXXFLAGS_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Failed
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> -- No external FFT libraries needed for the OpenMM build, using fftpack!
> -- Threads not compatible with OpenMM build, disabled!
> CMake Warning at CMakeLists.txt:183 (message):
>   CPU-based acceleration turned off, OpenMM does not support/need any!
>
>
> -- Looking for include files HAVE_STRING_H
> -- Looking for include files HAVE_STRING_H - found
> -- Looking for include files HAVE_MATH_H
> -- Looking for include files HAVE_MATH_H - found
> -- Looking for include files HAVE_LIMITS_H
> -- Looking for include files HAVE_LIMITS_H - found
> -- Looking for include files HAVE_MEMORY_H
> -- Looking for include files HAVE_MEMORY_H - found
> -- Looking for include files HAVE_UNISTD_H
> -- Looking for include files HAVE_UNISTD_H - found
> -- Looking for include files HAVE_PWD_H
> -- Looking for include files HAVE_PWD_H - found
> -- Looking for include files HAVE_STDINT_H
> -- Looking for include files HAVE_STDINT_H - found
> -- Looking for include files HAVE_STDLIB_H
> -- Looking for include files HAVE_STDLIB_H - found
> -- Looking for include files HAVE_PTHREAD_H
> -- Looking for include files HAVE_PTHREAD_H - found
> -- Looking for include files HAVE_DIRENT_H
> -- Looking for include files HAVE_DIRENT_H - found
> -- Looking for include files HAVE_INTTYPES_H
> -- Looking for include files HAVE_INTTYPES_H - found
> -- Looking for include files HAVE_REGEX_H
> -- Looking for include files HAVE_REGEX_H - found
> -- Looking for include files HAVE_SYS_TYPES_H
> -- Looking for include files HAVE_SYS_TYPES_H - found
> -- Looking for include files HAVE_SYS_STAT_H
> -- Looking for include files HAVE_SYS_STAT_H - found
> -- Looking for include files HAVE_SYS_TIME_H
> -- Looking for include files HAVE_SYS_TIME_H - found
> -- Looking for include files HAVE_RPC_RPC_H
> -- Looking for include files HAVE_RPC_RPC_H - found
> -- Looking for include files HAVE_RPC_XDR_H
> -- Looking for include files HAVE_RPC_XDR_H - found
> -- Looking for include files HAVE_XMMINTRIN_H
> -- Looking for include files HAVE_XMMINTRIN_H - found
> -- Looking for include files HAVE_EMMINTRIN_H
> -- Looking for include files HAVE_EMMINTRIN_H - found
> -- Looking for include files HAVE_PMMINTRIN_H
> -- Looking for include files HAVE_PMMINTRIN_H - not found.
> -- Looking for include files HAVE_SMMINTRIN_H
> -- Looking for include files HAVE_SMMINTRIN_H - not found.
> -- Looking for include files HAVE_IO_H
> -- Looking for include files HAVE_IO_H - not found.
> -- Looking for strcasecmp
> -- Looking for strcasecmp - found
> -- Looking for strdup
> -- Looking for strdup - found
> -- Looking for vprintf
> -- Looking

Re: [gmx-users] Hardware-specific crash with 4.5.1

[Justin A. Lemkul]

Roland Schulz wrote:



On Mon, Sep 27, 2010 at 9:58 PM, Mark Abraham > wrote:




- Original Message -
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Date: Tuesday, September 28, 2010 11:39
Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>

 >
 >
 > Mark Abraham wrote:
 > >
 > >
 > >- Original Message -
 > >From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
 > >Date: Tuesday, September 28, 2010 11:11
 > >Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1
 > >To: Gromacs Users' List mailto:gmx-users@gromacs.org>>
 > >
 > > >
 > > >
 > > > Roland Schulz wrote:
 > > > >Justin,
 > > > >
 > > > >I think the interaction kernel is not OK on your PowerPC
 > > > machine. I assume that from: 1) The force seems to be zero
 > > > (minimization output). 2) When you use the all-to-all kernel
 > > > which is not available for the powerpc kernel, it automatically
 > > > falls back to the C kernel and then it works.
 > > > >
 > > >
 > > > Sounds about right.
 > > >
 > > > >What is the kernel you are using? It should say in the log
 > > > file. Look for: "Configuring single precision IBM Power6-
 > > > specific Fortran kernels" or "Testing Altivec/VMX support"
 > > > >
 > > >
 > > > I'm not finding either in the config.log - weird?
 > >
 > >You were meant to look in the mdrun.log for runtime
 > confirmation of what kernels GROMACS has decided to use.
 > >
 >
 > That seems entirely obvious, now that you mention it :) 
 > Conveniently, I find the following in the md.log file from the

 > (failing) autoconf-assembled mdrun:
 >
 > Configuring nonbonded kernels...
 > Configuring standard C nonbonded kernels...
 > Testing Altivec/VMX support... present.
 > Configuring PPC/Altivec nonbonded kernels...
 >
 > The (non)MPI CMake build shows the following:
 >
 > Configuring nonbonded kernels...
 > Configuring standard C nonbonded kernels...
 >
 > So it seems clear to me that autoconf built faulty nonbonded
 > kernels, and CMake didn't.

OK, so assuming that PPC/Altivec kernels are supposed to be good for
Mac (as they were in 4.0.x, I believe):

1) CMake doesn't detect that it should be using those kernels, and
so appears to work, but does an inefficient run. autoconf detects
that it should use those kernels, but the mdrun fails for reasons
that are not yet clear.

 
 > > > >You can also look in the config.h whether  GMX_POWER6

 > > > and/or GMX_PPC_ALTIVEC is set. I suggest you try to compile with
 > > > one/both of them deactivated and see whether that solves it.
 > > > This will make it slower too. Thus if this is indeed the
 > > > problem, you will probably want to figure out why the fastest
 > > > kernel doesn't work correctly to get good performance.
 > > > >
 > > >
 > > > It looks like GMX_PPC_ALTIVEC is set.  I suppose I
 > could re-
 > > > compile with this turned off.
 > >
 > >This is supposed to be fine for Mac, as I understand.
 > >
 > > > Here's what's even weirder.  The problematic version was
 > > > compiled using the standard autoconf procedure.  If I
 > use a
 > > > CMake-compiled version, the energy minimization runs fine,
 > > > giving the same results (energy and force) as the two
 > systems I
 > > > know are good.  So I guess there's something wrong with the
 > > > way autoconf installed Gromacs.  Perhaps this isn't of
 > > > concern since Gromacs will require CMake in subsequent releases,
 > > > but I figure I should at least report it in case it affects
 > > > anyone else.
 > > >
 > > > If I may tack one more question on here, I'm wondering why my
 > > > CMake installation  doesn't actually appear to be using
 > > > MPI.  I get the right result, but the problem is, I get a
 > > > .log, .edr, and .trr for every processor that's being used, as
 > > > if each processor is being given its own job and not
 > > > distributing the work. Here's how I compiled my MPI mdrun,
 > > > version 4.5.1:
 > >
 > >At the start and end of the .log files you should get
 > indicators about how many MPI processes were actually being used.
 > >
 >
 > That explains it (sort of).  It looks like mdrun thinks
 > it's only being run over 1 node, just several times over, and a
 > bunch of junk that isn't getting written properly:
 >
 > Log file opened on Mon Sep 27 21:36:00 2010
 > Host: n235  pid: 6857  nodeid: 0  nnodes:  1
 > The Gromacs distribution was built @TMP_TIME@ by
 > jalem...@sysx2.arc-int.vt.edu
 [CMAKE] (@TMP_MACHI

Re: [gmx-users] topology file for two molecules

[Gavin Melaugh]

Justin

Cheers, I had just posted a more general query prior to you getting
back? It is perhaps not as vague.

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> I Did the following and it worked. You were right about using one atom
>> types directive. If you don't mind I have another query. In all my
>> topology files to date (one molecule type), I have always listed the
>> atomtypes in the [atomtypes] directive, and used the set up in
>> [defaults] below. Is this all that is required for the calculation of
>> the LJ energies. I have never used a pair list, a pair types directive
>> or a nonbond_params directive. From the output I still get LJ energies
>> but I am slightly confused by all the different options.
>>
>
> I can't give a better explanation than what is already in the manual,
> specifically section 5.3.3 ([nonbond_params] and whether or not you
> need it). Whether or not you need [pairs] depends on the underlying
> mechanics of the force field you're using.  See section 5.3.5.
>
> -Justin
>
>> parameter level
>> [defaults]
>> ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ
>>  1 3  yes0.5 0.5
>>
>> [atomtypes]
>> ;type mass   charge  ptype sigma(nm)   
>> epsilon(kjmol-1)
>>CB 12.011000  0.00   A  0.355000  0.292880
>>CA 12.011000 -0.115000   A  0.355000  0.292880
>>HC  1.008000  0.115000   A  0.242000  0.125520
>>CU 13.019000  0.265000   A  0.35  0.334720
>>NU 14.007000 -0.597000   A  0.325000  0.711280
>>CH 13.019000  0.332000   A  0.385000  0.334720
>>C3 15.035000  0.00   A  0.390500  0.732200
>>CT 12.011000 -0.18   A  0.35  0.276144
>>HH  1.008000  0.06   A  0.25  0.125520
>>
>> #include "tertpentane.itp"
>> #include "methylcage.itp"
>>
>> ;System level
>> [system]
>> ;the name of this system
>> cage and pentane
>>
>> [molecules]
>> ; moleculename number
>>  tertpentane  1
>>  methylcage   1
>>
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Hi Justin

 Cheers. I have attached my pentane itp file. The cage itp is formatted
 the same. In the examples there never seems to be [atom types]
 included.
 I have included it. Does it seem O.K?

>>> You only need to use an [atomtypes] directive if you're introducing
>>> new atom types into the force field.  I don't know if it's
>>> necessary. I also don't know if these sections can be discontinuous
>>> (i.e., one
>>> section present in cage.itp, another in tertpentane.itp).  Try the
>>> approach I sent you and see.  If you get fatal errors, then you may
>>> have to assemble a single [atomtypes] directive and put it either in
>>> the first .itp file you #include, or before any of the #includes in
>>> the .top (since #include really just means "cut-and-paste the stuff
>>> here," it works the same).
>>>
>>> -Justin
>>>
 Gavin

 Justin A. Lemkul wrote:
> Gavin Melaugh wrote:
>> Hi Mark.
>>
>> I have looked this up, but I am a little uncertain. Does one of the
>> topologies have to be included within the other as an .itp file.
>> If so
> No.  You #include .itp files to simply add molecules within a
> .top; it
> would be very rare to #include an .itp within an .itp (although it
> can
> be done).  For your case, your .top is simple:
>
> #include (force field)
>
> #include "cage.itp"
> #include "pentane.itp"
>
> [ system ]
> My system
>
> [ molecules ]
> Cage1
> Pentane 1
>
>> do I only define the [defaults directive] in the .top file i.e. I
>> take
>> it I don't include this directive in the .itp file as well.
>>
> The [defaults] directive is provided by whatever force field you
> #include.  If you're using some custom parameters, then it needs
> to be
> defined once (and only once) at the top of your .top file. 
> Otherwise,
> you'll get fatal errors from grompp.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Mark Abraham wrote:
>>> Look up the include file mechanism on the webpage.
>>>
>>> Mark
>>>
>>> - Original Message -
>>> From: Gavin Melaugh 
>>> Date: Tuesday, September 28, 2010 19:04
>>> Subject: [gmx-users] topology file for two molecules
>>> To: Discussion list for GROMACS users 
>>>
 Hi all

 I want to run a simulation of one tert-pentane molecule inside one
 organic cage molecule. I have the topology files for both
 molecules but
 obviously I only need one .top file as the input for grompp.
 What is the
 most convenient way of having both topologies in one f

[gmx-users] non-bonding parameters

[Gavin Melaugh]

Hi all

I need some clarification on a few matters please. I have always used topology 
files (for one molecule) with the following format (below with values 
excluded). 
Does the format below enable LJ energies to be calculated?
Does it enable 1,4 interactions to be calculated? (In reference to gen-pair = 
yes.) Do I need a pair list or the following directives [nonbond_params] and 
[pairtypes]. I have always assumed that all LJ interactions both bonded 1,4 and 
non-bonded would be calculated from the parameters in the atomtypes directive 
using the corresponding comb rule.


Many Thanks 

Gavin

parameter level
[defaults]
; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ
 1 3  yes0.5 0.5

[atomtypes]
;type mass   charge  ptype sigma(nm) epsilon(kjmol-1)


;Molecular level
[moleculetype]
;   name nrexcl
tertpentane  3


[atoms]
; atomnr  type   resnr  residue   namecgnr charge mass


[bonds]
;  aiaj   func   b0(nm)   kb(kjmol-1 nm-2)


[angles]
;  aiajak   func  theta(deg)ktheta(kjmol-1 rad-2)


[dihedrals]


;System level
[system]


[molecules]
; moleculename number





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Re: [gmx-users] topology file for two molecules

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi Justin

I Did the following and it worked. You were right about using one atom
types directive. If you don't mind I have another query. In all my
topology files to date (one molecule type), I have always listed the
atomtypes in the [atomtypes] directive, and used the set up in
[defaults] below. Is this all that is required for the calculation of
the LJ energies. I have never used a pair list, a pair types directive
or a nonbond_params directive. From the output I still get LJ energies
but I am slightly confused by all the different options.



I can't give a better explanation than what is already in the manual, 
specifically section 5.3.3 ([nonbond_params] and whether or not you need it). 
Whether or not you need [pairs] depends on the underlying mechanics of the force 
field you're using.  See section 5.3.5.


-Justin


parameter level
[defaults]
; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ
 1 3  yes0.5 0.5

[atomtypes]
;type mass   charge  ptype sigma(nm)
epsilon(kjmol-1)

   CB 12.011000  0.00   A  0.355000  0.292880
   CA 12.011000 -0.115000   A  0.355000  0.292880
   HC  1.008000  0.115000   A  0.242000  0.125520
   CU 13.019000  0.265000   A  0.35  0.334720
   NU 14.007000 -0.597000   A  0.325000  0.711280
   CH 13.019000  0.332000   A  0.385000  0.334720
   C3 15.035000  0.00   A  0.390500  0.732200
   CT 12.011000 -0.18   A  0.35  0.276144
   HH  1.008000  0.06   A  0.25  0.125520

#include "tertpentane.itp"
#include "methylcage.itp"

;System level
[system]
;the name of this system
cage and pentane

[molecules]
; moleculename number
 tertpentane  1
 methylcage   1


Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Hi Justin

Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?


You only need to use an [atomtypes] directive if you're introducing
new atom types into the force field.  I don't know if it's necessary. 
I also don't know if these sections can be discontinuous (i.e., one

section present in cage.itp, another in tertpentane.itp).  Try the
approach I sent you and see.  If you get fatal errors, then you may
have to assemble a single [atomtypes] directive and put it either in
the first .itp file you #include, or before any of the #includes in
the .top (since #include really just means "cut-and-paste the stuff
here," it works the same).

-Justin


Gavin

Justin A. Lemkul wrote:

Gavin Melaugh wrote:

Hi Mark.

I have looked this up, but I am a little uncertain. Does one of the
topologies have to be included within the other as an .itp file. If so

No.  You #include .itp files to simply add molecules within a .top; it
would be very rare to #include an .itp within an .itp (although it can
be done).  For your case, your .top is simple:

#include (force field)

#include "cage.itp"
#include "pentane.itp"

[ system ]
My system

[ molecules ]
Cage1
Pentane 1


do I only define the [defaults directive] in the .top file i.e. I take
it I don't include this directive in the .itp file as well.


The [defaults] directive is provided by whatever force field you
#include.  If you're using some custom parameters, then it needs to be
defined once (and only once) at the top of your .top file.  Otherwise,
you'll get fatal errors from grompp.

-Justin


Cheers

Gavin

Mark Abraham wrote:

Look up the include file mechanism on the webpage.

Mark

- Original Message -
From: Gavin Melaugh 
Date: Tuesday, September 28, 2010 19:04
Subject: [gmx-users] topology file for two molecules
To: Discussion list for GROMACS users 


Hi all

I want to run a simulation of one tert-pentane molecule inside one
organic cage molecule. I have the topology files for both
molecules but
obviously I only need one .top file as the input for grompp.
What is the
most convenient way of having both topologies in one file?

Many Thanks

Gavin
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--


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


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Re: [gmx-users] Reg: Liquid-liquid interface simulation

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:
why don't someone can post the tutorial in the gromacs website? because 


The implication from my previous message was that, if you cannot find a tutorial 
in an obvious place, one does not exist.  There is not a tutorial for every task 
that a user may wish to undertake; such a feat would be impossible.


gromacs was heavily used for liquid-liquid interface simulation.I hope 
probably i will do it in the near future.
 


Just because the software has been used for a specific purpose does not 
necessitate the existence of a tutorial.  People who do the simulations do not 
always have the time to write up (and subsequently maintain) tutorial materials.


If you come up with a tutorial, please post it to the Gromacs site.

-Justin


Regards
Vinoth

On Tue, Sep 28, 2010 at 4:05 PM, Justin A. Lemkul > wrote:




vinothkumar mohanakrishnan wrote:

Is there any tutorial for liquid-liquid interface in any of the
website?.
 



If you can't find it at
http://www.gromacs.org/Documentation/Tutorials or with Google, then
it probably doesn't exist.

-Justin

Regards
Vinoth


On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>
>> wrote:

   On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote:

   Hi all

   Is that any one have liquid-liquid interface simulation (like
   lysozyme
   by justin). if so kindly share it through this discussiion
   forum.it  
    >
will be of great help for

   the newusers like me to use

   gromacs for liquid-liquid interface simulation.

   Regards
   Vinoth

   We prefer to keep discussions on the mailing list for more direct
   impact and for archiving purposes. If there are tutorials or
howtos
   on certain topics they can be uploaded to the website.

   -- David van der Spoel, Ph.D., Professor of Biology
   Dept. of Cell & Molec. Biol., Uppsala University.
   Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
   sp...@xray.bmc.uu.se 
>
  http://folding.bmc.uu.se 



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

   >

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


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


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Re: [gmx-users] Grompp Error : Segmentation fault

[Florian Dommert]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello,

 I am really curious that amber has support for Room Temperature Ionic
liquids ? Can you please provide me a reference how this force field
works for this kind of liquids.

/Flo



On 09/28/2010 03:01 PM, Alep Latep wrote:
> Dear Gromacs Users and Developers,
> 
> I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my
> ionic liquid MD simulation using amber 99 force field. I got my topology
> from topolbuild v 1.3. I successfully minimized both cation and anion
> separately using cg and steep. Then I include the anion in the cation
> system using genbox. I got error from grompp like this: 
> --
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> processing topology...
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Segmentation fault (core dumped)
> [a...@neox MD1]$ 
> -
> Still cant find my answer in the mailing list. Sorry for the large post,
> but here's my .mdp and .top
> 
> -
> title = Conjugated-Gradients Energy Minimization
> 
> ; Preprocessing
> cpp = /lib/cpp
> include = -I../top
> 
> ; Parameters
> integrator = cg
> emtol = 1.0
> nsteps = 5000
> nstenergy = 100
> nstxtcout = 100
> xtc_grps = System
> energygrps = System
> 
> ; Neighboursearching
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> constraints = none
> pbc = xyz
> -
> ; Topology from .mol2 file
> ; topolbuild version 1.3
> ; Command line:
> ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
> ;
> ; The force field files to be included
> #include "amber99.ff/forcefield.itp"
> 
>  [ moleculetype ]
> ; name  nrexcl
> BMIM   3
> 
>  [ atoms ]
> ;  nrtype   resnr   residu   atom   cgnrcharge  mass
> 1  CT 1  BMIM   C1  -0.17243  12.01100  
> ;  -0.1724300
> 2  HC 1  BMIM   H1   0.07139   1.00800  
> ;  -0.1010400
> 3  HC 1  BMIM   H1   0.05434   1.00800  
> ;  -0.0467000
> 4  HC 1  BMIM   H1   0.05138   1.00800  
> ;   0.0046800
> 5  CT 1  BMIM   C2   0.02353  12.01100  
> ;   0.0282100
> 6  HC 1  BMIM   H2   0.02417   1.00800  
> ;   0.0523800
> 7  HC 1  BMIM   H2   0.02427   1.00800  
> ;   0.0766500
> 8  CT 1  BMIM   C3   0.01014  12.01100  
> ;   0.0867900
> 9  HC 1  BMIM   H3   0.03312   1.00800  
> ;   0.1199100
>10  HC 1  BMIM   H3   0.02952   1.00800  
> ;   0.1494300
>11  NA 1  BMIM   N4   0.05435  14.00670  
> ;   0.2037800
>12  CC 1  BMIM   C4  -0.17380  12.01100  
> ;   0.0299800
>13  H4 1  BMIM   H4   0.23709   1.00800  
> ;   0.2670700
>14  NA 1  BMIM   N6   0.07275  14.00670  
> ;   0.3398200
>15  CT 1  BMIM   C5  -0.07367  12.01100  
> ;   0.2661500
>16  H1 1  BMIM   H5   0.10657   1.00800  
> ;   0.3727200
>17  H1 1  BMIM   H5   0.09108   1.00800  
> ;   0.4638000
>18  CC 1  BMIM   C6  -0.08433  12.01100  
> ;   0.3794700
>19  H4 1  BMIM   H6   0.20500   1.00800  
> ;   0.5844700
>20  CR 1  BMIM   C7  -0.02624  12.01100  
> ;   0.5582300
>21  H5 1  BMIM   H7   0.21862   1.00800  
> ;   0.7768500
>22  CT 1  BMIM   C8  -0.18403  12.01100  
> ;   0.5928200
>23  H1 1  BMIM   H8   0.13823   1.00800  
> ;   0.7310500
>24  H1 1  BMIM   H8   0.13886   1.00800  
> ;   0.8699100
>25  H1 1  BMIM   H8   0.13010   1.00800  
> ;   1.100
> ; total molecule charge =   1.100
> 
>  [ bonds ]
> ;   ai  aj   funct  b0  kb
>1 5   1 0.15260  259408.   ; C- C
>1 2   1 0.10900  284512.   ; C- H
>1 3   1 0.10900  284512.   ; C- H
>1 4   1 0.10900  284512.   ; C- H
>5 8   1 0.15260  259408.   ; C- C
>5 6   1 0.10900  284511.   ; C

Re: [gmx-users] topology file for two molecules

[Gavin Melaugh]

Hi Justin

I Did the following and it worked. You were right about using one atom
types directive. If you don't mind I have another query. In all my
topology files to date (one molecule type), I have always listed the
atomtypes in the [atomtypes] directive, and used the set up in
[defaults] below. Is this all that is required for the calculation of
the LJ energies. I have never used a pair list, a pair types directive
or a nonbond_params directive. From the output I still get LJ energies
but I am slightly confused by all the different options.

parameter level
[defaults]
; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ
 1 3  yes0.5 0.5

[atomtypes]
;type mass   charge  ptype sigma(nm)
epsilon(kjmol-1)
   CB 12.011000  0.00   A  0.355000  0.292880
   CA 12.011000 -0.115000   A  0.355000  0.292880
   HC  1.008000  0.115000   A  0.242000  0.125520
   CU 13.019000  0.265000   A  0.35  0.334720
   NU 14.007000 -0.597000   A  0.325000  0.711280
   CH 13.019000  0.332000   A  0.385000  0.334720
   C3 15.035000  0.00   A  0.390500  0.732200
   CT 12.011000 -0.18   A  0.35  0.276144
   HH  1.008000  0.06   A  0.25  0.125520

#include "tertpentane.itp"
#include "methylcage.itp"

;System level
[system]
;the name of this system
cage and pentane

[molecules]
; moleculename number
 tertpentane  1
 methylcage   1


Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Cheers. I have attached my pentane itp file. The cage itp is formatted
>> the same. In the examples there never seems to be [atom types] included.
>> I have included it. Does it seem O.K?
>>
>
> You only need to use an [atomtypes] directive if you're introducing
> new atom types into the force field.  I don't know if it's necessary. 
> I also don't know if these sections can be discontinuous (i.e., one
> section present in cage.itp, another in tertpentane.itp).  Try the
> approach I sent you and see.  If you get fatal errors, then you may
> have to assemble a single [atomtypes] directive and put it either in
> the first .itp file you #include, or before any of the #includes in
> the .top (since #include really just means "cut-and-paste the stuff
> here," it works the same).
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Hi Mark.

 I have looked this up, but I am a little uncertain. Does one of the
 topologies have to be included within the other as an .itp file. If so
>>> No.  You #include .itp files to simply add molecules within a .top; it
>>> would be very rare to #include an .itp within an .itp (although it can
>>> be done).  For your case, your .top is simple:
>>>
>>> #include (force field)
>>>
>>> #include "cage.itp"
>>> #include "pentane.itp"
>>>
>>> [ system ]
>>> My system
>>>
>>> [ molecules ]
>>> Cage1
>>> Pentane 1
>>>
 do I only define the [defaults directive] in the .top file i.e. I take
 it I don't include this directive in the .itp file as well.

>>> The [defaults] directive is provided by whatever force field you
>>> #include.  If you're using some custom parameters, then it needs to be
>>> defined once (and only once) at the top of your .top file.  Otherwise,
>>> you'll get fatal errors from grompp.
>>>
>>> -Justin
>>>
 Cheers

 Gavin

 Mark Abraham wrote:
> Look up the include file mechanism on the webpage.
>
> Mark
>
> - Original Message -
> From: Gavin Melaugh 
> Date: Tuesday, September 28, 2010 19:04
> Subject: [gmx-users] topology file for two molecules
> To: Discussion list for GROMACS users 
>
>> Hi all
>>
>> I want to run a simulation of one tert-pentane molecule inside one
>> organic cage molecule. I have the topology files for both
>> molecules but
>> obviously I only need one .top file as the input for grompp.
>> What is the
>> most convenient way of having both topologies in one file?
>>
>> Many Thanks
>>
>> Gavin
>> -- 
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
>>
>

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[gmx-users] Grompp Error : Segmentation fault

[Alep Latep]

Dear Gromacs Users and Developers,

I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic
liquid MD simulation using amber 99 force field. I got my topology from
topolbuild v 1.3. I successfully minimized both cation and anion separately
using cg and steep. Then I include the anion in the cation system using
genbox. I got error from grompp like this:
--
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Segmentation fault (core dumped)
[a...@neox MD1]$
-
Still cant find my answer in the mailing list. Sorry for the large post, but
here's my .mdp and .top

-
title = Conjugated-Gradients Energy Minimization

; Preprocessing
cpp = /lib/cpp
include = -I../top

; Parameters
integrator = cg
emtol = 1.0
nsteps = 5000
nstenergy = 100
nstxtcout = 100
xtc_grps = System
energygrps = System

; Neighboursearching
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
constraints = none
pbc = xyz
-
; Topology from .mol2 file
; topolbuild version 1.3
; Command line:
; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
;
; The force field files to be included
#include "amber99.ff/forcefield.itp"

 [ moleculetype ]
; name  nrexcl
BMIM   3

 [ atoms ]
;  nrtype   resnr   residu   atom   cgnrcharge  mass
1  CT 1  BMIM   C1  -0.17243  12.01100   ;
 -0.1724300
2  HC 1  BMIM   H1   0.07139   1.00800   ;
 -0.1010400
3  HC 1  BMIM   H1   0.05434   1.00800   ;
 -0.0467000
4  HC 1  BMIM   H1   0.05138   1.00800   ;
0.0046800
5  CT 1  BMIM   C2   0.02353  12.01100   ;
0.0282100
6  HC 1  BMIM   H2   0.02417   1.00800   ;
0.0523800
7  HC 1  BMIM   H2   0.02427   1.00800   ;
0.0766500
8  CT 1  BMIM   C3   0.01014  12.01100   ;
0.0867900
9  HC 1  BMIM   H3   0.03312   1.00800   ;
0.1199100
   10  HC 1  BMIM   H3   0.02952   1.00800   ;
0.1494300
   11  NA 1  BMIM   N4   0.05435  14.00670   ;
0.2037800
   12  CC 1  BMIM   C4  -0.17380  12.01100   ;
0.0299800
   13  H4 1  BMIM   H4   0.23709   1.00800   ;
0.2670700
   14  NA 1  BMIM   N6   0.07275  14.00670   ;
0.3398200
   15  CT 1  BMIM   C5  -0.07367  12.01100   ;
0.2661500
   16  H1 1  BMIM   H5   0.10657   1.00800   ;
0.3727200
   17  H1 1  BMIM   H5   0.09108   1.00800   ;
0.4638000
   18  CC 1  BMIM   C6  -0.08433  12.01100   ;
0.3794700
   19  H4 1  BMIM   H6   0.20500   1.00800   ;
0.5844700
   20  CR 1  BMIM   C7  -0.02624  12.01100   ;
0.5582300
   21  H5 1  BMIM   H7   0.21862   1.00800   ;
0.7768500
   22  CT 1  BMIM   C8  -0.18403  12.01100   ;
0.5928200
   23  H1 1  BMIM   H8   0.13823   1.00800   ;
0.7310500
   24  H1 1  BMIM   H8   0.13886   1.00800   ;
0.8699100
   25  H1 1  BMIM   H8   0.13010   1.00800   ;
1.100
; total molecule charge =   1.100

 [ bonds ]
;   ai  aj   funct  b0  kb
   1 5   1 0.15260  259408.   ; C- C
   1 2   1 0.10900  284512.   ; C- H
   1 3   1 0.10900  284512.   ; C- H
   1 4   1 0.10900  284512.   ; C- H
   5 8   1 0.15260  259408.   ; C- C
   5 6   1 0.10900  284511.   ; C- H
   5 7   1 0.10900  284512.   ; C- H
   815   1 0.15260  259408.   ; C- C
   8 9   1 0.10900  284512.   ; C- H
   810   1 0.10900  284512.   ; C- H
  1112   1 0.13850  353129.   ; N- C
  1115   1 0.13850  353129.   ; N- C
  1120   1 0.13850  353129.   ; N- C
  1218   1 0.14000  392459.   ; C- C
  1213   1 0.10800  

Re: [gmx-users] Salt concentration

[Anthony Cruz Balberdi]

Thank you Gonçalo and Dallas for your help.

Best Regards

Anthony

2010/9/27 Gonçalo C. Justino :
> Hi Anthony,
> You can use the '-conc' tag from genion during file preparation, as
> per http://manual.gromacs.org/current/online/genion.html.
> Gonçalo
>
> On 27 September 2010 15:32, Anthony Cruz Balberdi 
> wrote:
>>
>> Dear Users:
>> I am interested in perform a simulation of a protein in different salt
>> concentrations. How I can calculate how much Na+ and Cl- ions to
>> include in the simulation to achieve certain concentration? Could
>> someone point me in the right direction? Is there a software to do
>> this type of calculations?
>>
>> Thanks in advance.
>>
>> Anthony
>> --
>> gmx-users mailing list    gmx-us...@gromacs.org
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>
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Re: [gmx-users] topology file for two molecules

[Gavin Melaugh]

O.K

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Cheers. I have attached my pentane itp file. The cage itp is formatted
>> the same. In the examples there never seems to be [atom types] included.
>> I have included it. Does it seem O.K?
>>
>
> You only need to use an [atomtypes] directive if you're introducing
> new atom types into the force field.  I don't know if it's necessary. 
> I also don't know if these sections can be discontinuous (i.e., one
> section present in cage.itp, another in tertpentane.itp).  Try the
> approach I sent you and see.  If you get fatal errors, then you may
> have to assemble a single [atomtypes] directive and put it either in
> the first .itp file you #include, or before any of the #includes in
> the .top (since #include really just means "cut-and-paste the stuff
> here," it works the same).
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> Gavin Melaugh wrote:
 Hi Mark.

 I have looked this up, but I am a little uncertain. Does one of the
 topologies have to be included within the other as an .itp file. If so
>>> No.  You #include .itp files to simply add molecules within a .top; it
>>> would be very rare to #include an .itp within an .itp (although it can
>>> be done).  For your case, your .top is simple:
>>>
>>> #include (force field)
>>>
>>> #include "cage.itp"
>>> #include "pentane.itp"
>>>
>>> [ system ]
>>> My system
>>>
>>> [ molecules ]
>>> Cage1
>>> Pentane 1
>>>
 do I only define the [defaults directive] in the .top file i.e. I take
 it I don't include this directive in the .itp file as well.

>>> The [defaults] directive is provided by whatever force field you
>>> #include.  If you're using some custom parameters, then it needs to be
>>> defined once (and only once) at the top of your .top file.  Otherwise,
>>> you'll get fatal errors from grompp.
>>>
>>> -Justin
>>>
 Cheers

 Gavin

 Mark Abraham wrote:
> Look up the include file mechanism on the webpage.
>
> Mark
>
> - Original Message -
> From: Gavin Melaugh 
> Date: Tuesday, September 28, 2010 19:04
> Subject: [gmx-users] topology file for two molecules
> To: Discussion list for GROMACS users 
>
>> Hi all
>>
>> I want to run a simulation of one tert-pentane molecule inside one
>> organic cage molecule. I have the topology files for both
>> molecules but
>> obviously I only need one .top file as the input for grompp.
>> What is the
>> most convenient way of having both topologies in one file?
>>
>> Many Thanks
>>
>> Gavin
>> -- 
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
>>
>

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Re: [gmx-users] Reg: Liquid-liquid interface simulation

[vinothkumar mohanakrishnan]

why don't someone can post the tutorial in the gromacs website? because
gromacs was heavily used for liquid-liquid interface simulation.I hope
probably i will do it in the near future.

Regards
Vinoth

On Tue, Sep 28, 2010 at 4:05 PM, Justin A. Lemkul  wrote:

>
>
> vinothkumar mohanakrishnan wrote:
>
>> Is there any tutorial for liquid-liquid interface in any of the website?.
>>
>>
>
> If you can't find it at http://www.gromacs.org/Documentation/Tutorials or
> with Google, then it probably doesn't exist.
>
> -Justin
>
> Regards
>> Vinoth
>>
>>
>> On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel <
>> sp...@xray.bmc.uu.se > wrote:
>>
>>On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote:
>>
>>Hi all
>>
>>Is that any one have liquid-liquid interface simulation (like
>>lysozyme
>>by justin). if so kindly share it through this discussiion
>>forum.it 
>>> will be of great help for
>>
>>the newusers like me to use
>>
>>gromacs for liquid-liquid interface simulation.
>>
>>Regards
>>Vinoth
>>
>>We prefer to keep discussions on the mailing list for more direct
>>impact and for archiving purposes. If there are tutorials or howtos
>>on certain topics they can be uploaded to the website.
>>
>>-- David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>> http://folding.bmc.uu.se 
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> --
> 
>
> 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
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>
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Re: [gmx-users] topology file for two molecules

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi Justin

Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?



You only need to use an [atomtypes] directive if you're introducing new atom 
types into the force field.  I don't know if it's necessary.  I also don't know 
if these sections can be discontinuous (i.e., one section present in cage.itp, 
another in tertpentane.itp).  Try the approach I sent you and see.  If you get 
fatal errors, then you may have to assemble a single [atomtypes] directive and 
put it either in the first .itp file you #include, or before any of the 
#includes in the .top (since #include really just means "cut-and-paste the stuff 
here," it works the same).


-Justin


Gavin

Justin A. Lemkul wrote:


Gavin Melaugh wrote:

Hi Mark.

I have looked this up, but I am a little uncertain. Does one of the
topologies have to be included within the other as an .itp file. If so

No.  You #include .itp files to simply add molecules within a .top; it
would be very rare to #include an .itp within an .itp (although it can
be done).  For your case, your .top is simple:

#include (force field)

#include "cage.itp"
#include "pentane.itp"

[ system ]
My system

[ molecules ]
Cage1
Pentane 1


do I only define the [defaults directive] in the .top file i.e. I take
it I don't include this directive in the .itp file as well.


The [defaults] directive is provided by whatever force field you
#include.  If you're using some custom parameters, then it needs to be
defined once (and only once) at the top of your .top file.  Otherwise,
you'll get fatal errors from grompp.

-Justin


Cheers

Gavin

Mark Abraham wrote:

Look up the include file mechanism on the webpage.

Mark

- Original Message -
From: Gavin Melaugh 
Date: Tuesday, September 28, 2010 19:04
Subject: [gmx-users] topology file for two molecules
To: Discussion list for GROMACS users 


Hi all

I want to run a simulation of one tert-pentane molecule inside one
organic cage molecule. I have the topology files for both
molecules but
obviously I only need one .top file as the input for grompp.
What is the
most convenient way of having both topologies in one file?

Many Thanks

Gavin
--
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--


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


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Re: [gmx-users] topology file for two molecules

[Gavin Melaugh]

Hi Justin

Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Mark.
>>
>> I have looked this up, but I am a little uncertain. Does one of the
>> topologies have to be included within the other as an .itp file. If so
>
> No.  You #include .itp files to simply add molecules within a .top; it
> would be very rare to #include an .itp within an .itp (although it can
> be done).  For your case, your .top is simple:
>
> #include (force field)
>
> #include "cage.itp"
> #include "pentane.itp"
>
> [ system ]
> My system
>
> [ molecules ]
> Cage1
> Pentane 1
>
>> do I only define the [defaults directive] in the .top file i.e. I take
>> it I don't include this directive in the .itp file as well.
>>
>
> The [defaults] directive is provided by whatever force field you
> #include.  If you're using some custom parameters, then it needs to be
> defined once (and only once) at the top of your .top file.  Otherwise,
> you'll get fatal errors from grompp.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Mark Abraham wrote:
>>> Look up the include file mechanism on the webpage.
>>>
>>> Mark
>>>
>>> - Original Message -
>>> From: Gavin Melaugh 
>>> Date: Tuesday, September 28, 2010 19:04
>>> Subject: [gmx-users] topology file for two molecules
>>> To: Discussion list for GROMACS users 
>>>
 Hi all

 I want to run a simulation of one tert-pentane molecule inside one
 organic cage molecule. I have the topology files for both
 molecules but
 obviously I only need one .top file as the input for grompp.
 What is the
 most convenient way of having both topologies in one file?

 Many Thanks

 Gavin
 -- 
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
>>
>

[atomtypes]
;type mass   charge  ptype sigma(nm) epsilon(kjmol-1)
   CT 12.011000 -0.18   A  0.35  0.276144
   HC  1.008000  0.06   A  0.25  0.125520

;Molecular level
[moleculetype]
;   name nrexcl
tertpentane  3

[atoms]
; atomnr  type   resnr  residue   namecgnr charge mass
1  CT   1PENT  CT   1  0. 12.0110
2  CT   1PENT  CT   1 -0.1800 12.0110
3  CT   1PENT  CT   1 -0.1800 12.0110
4  CT   1PENT  CT   1 -0.1800 12.0110
5  CT   1PENT  CT   1 -0.1800 12.0110
6  HC   1PENT  HC   1  0.0600  1.0080
7  HC   1PENT  HC   1  0.0600  1.0080
8  HC   1PENT  HC   1  0.0600  1.0080
9  HC   1PENT  HC   1  0.0600  1.0080
   10  HC   1PENT  HC   1  0.0600  1.0080
   11  HC   1PENT  HC   1  0.0600  1.0080
   12  HC   1PENT  HC   1  0.0600  1.0080
   13  HC   1PENT  HC   1  0.0600  1.0080
   14  HC   1PENT  HC   1  0.0600  1.0080
   15  HC   1PENT  HC   1  0.0600  1.0080
   16  HC   1PENT  HC   1  0.0600  1.0080
   17  HC   1PENT  HC   1  0.0600  1.0080

[bonds]
;  aiaj   func   b0(nm)   kb(kjmol-1 nm-2)
1 2 1 0.1529  224262.4
1 3 1 0.1529  224262.4
1 4 1 0.1529  224262.4
1 5 1 0.1529  224262.4
2 6 1 0.1090  284512.0
2 7 1 0.1090  284512.0
2 8 1 0.1090  284512.0
3 9 1 0.1090  284512.0
310 1 0.1090  284512.0
311 1 0.1090  284512.0
412 1 0.1090  284512.0
413 1 0.1090  284512.0
414 1 0.1090  284512.0
515 1 0.1090  284512.0
516 1 0.1090  284512.0
517 1 0.1090  284512.0

[angles]
;  aiajak   func  theta(deg)ktheta(kjmol-1 rad-2)
2 1 3 1 112.70  488.2728
2 1 4 1 112.70  488.2728
2 1 5 1 112.70  488.2728
3 1 4 1 112.70  488.2728
3 1 5 1 112.70  488.2728 
4 1 5 1 112.70  488.2728
1 2 6 1

Re: [gmx-users] topology file for two molecules

[Justin A. Lemkul]

Gavin Melaugh wrote:

Hi Mark.

I have looked this up, but I am a little uncertain. Does one of the
topologies have to be included within the other as an .itp file. If so


No.  You #include .itp files to simply add molecules within a .top; it would be 
very rare to #include an .itp within an .itp (although it can be done).  For 
your case, your .top is simple:


#include (force field)

#include "cage.itp"
#include "pentane.itp"

[ system ]
My system

[ molecules ]
Cage1
Pentane 1


do I only define the [defaults directive] in the .top file i.e. I take
it I don't include this directive in the .itp file as well.



The [defaults] directive is provided by whatever force field you #include.  If 
you're using some custom parameters, then it needs to be defined once (and only 
once) at the top of your .top file.  Otherwise, you'll get fatal errors from grompp.


-Justin


Cheers

Gavin

Mark Abraham wrote:

Look up the include file mechanism on the webpage.

Mark

- Original Message -
From: Gavin Melaugh 
Date: Tuesday, September 28, 2010 19:04
Subject: [gmx-users] topology file for two molecules
To: Discussion list for GROMACS users 


Hi all

I want to run a simulation of one tert-pentane molecule inside one
organic cage molecule. I have the topology files for both
molecules but
obviously I only need one .top file as the input for grompp.
What is the
most convenient way of having both topologies in one file?

Many Thanks

Gavin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 




--


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] Reg: Liquid-liquid interface simulation

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:

Is there any tutorial for liquid-liquid interface in any of the website?.
 


If you can't find it at http://www.gromacs.org/Documentation/Tutorials or with 
Google, then it probably doesn't exist.


-Justin


Regards
Vinoth

On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:


On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote:

Hi all

Is that any one have liquid-liquid interface simulation (like
lysozyme
by justin). if so kindly share it through this discussiion
forum.it 
> will be of great help for
the newusers like me to use

gromacs for liquid-liquid interface simulation.

Regards
Vinoth

We prefer to keep discussions on the mailing list for more direct
impact and for archiving purposes. If there are tutorials or howtos
on certain topics they can be uploaded to the website.

-- 
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se   
 http://folding.bmc.uu.se 
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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
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Re: [gmx-users] Reg: Liquid-liquid interface simulation

[vinothkumar mohanakrishnan]

Is there any tutorial for liquid-liquid interface in any of the website?.

Regards
Vinoth

On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel
wrote:

> On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote:
>
>> Hi all
>>
>> Is that any one have liquid-liquid interface simulation (like lysozyme
>> by justin). if so kindly share it through this discussiion forum.it
>>  will be of great help for the newusers like me to use
>>
>> gromacs for liquid-liquid interface simulation.
>>
>> Regards
>> Vinoth
>>
>> We prefer to keep discussions on the mailing list for more direct impact
> and for archiving purposes. If there are tutorials or howtos on certain
> topics they can be uploaded to the website.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] topology file for two molecules

[Gavin Melaugh]

Hi Mark.

I have looked this up, but I am a little uncertain. Does one of the
topologies have to be included within the other as an .itp file. If so
do I only define the [defaults directive] in the .top file i.e. I take
it I don't include this directive in the .itp file as well.

Cheers

Gavin

Mark Abraham wrote:
> Look up the include file mechanism on the webpage.
>
> Mark
>
> - Original Message -
> From: Gavin Melaugh 
> Date: Tuesday, September 28, 2010 19:04
> Subject: [gmx-users] topology file for two molecules
> To: Discussion list for GROMACS users 
>
> > Hi all
> >
> > I want to run a simulation of one tert-pentane molecule inside one
> > organic cage molecule. I have the topology files for both
> > molecules but
> > obviously I only need one .top file as the input for grompp.
> > What is the
> > most convenient way of having both topologies in one file?
> >
> > Many Thanks
> >
> > Gavin
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] topology file for two molecules

[Mark Abraham]

Look up the include file mechanism on the webpage.

Mark

- Original Message -
From: Gavin Melaugh 
Date: Tuesday, September 28, 2010 19:04
Subject: [gmx-users] topology file for two molecules
To: Discussion list for GROMACS users 

> Hi all
> 
> I want to run a simulation of one tert-pentane molecule inside one
> organic cage molecule. I have the topology files for both 
> molecules but
> obviously I only need one .top file as the input for grompp. 
> What is the
> most convenient way of having both topologies in one file?
> 
> Many Thanks
> 
> Gavin
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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RE: [gmx-users] g_rdf normalization

[Berk Hess]

Hi,

g_rdf -surf mol counts the number of atoms within a distance r from the surface,
i.e. the atoms which have a distance of less than r to the closest atom of the 
molecule.
Since the surface can be complex and dynamic, normalization is difficult.

Berk

From: ch...@nus.edu.sg
To: gmx-users@gromacs.org
Date: Tue, 28 Sep 2010 16:38:58 +0800
Subject: [gmx-users] g_rdf normalization
















Dear fellow Gromacs users

Does anyone know how the “–surf mol”
option works?

 

I am trying to calculate the coordination number for a
molecule in a slice (xy-plane, delta-z ~ 0.5 nm) of my system. I believe I 
understand
how to do the integration of the RDF function if I use the center-of-mass
option (-rdf mol_com), but I am more interested in calculating the coordination
number with respect to the molecular surface. I have tried to use the “–surf
mol” option together with “–cn “, and I get what I
expected to get, namely N=2. However, when I import the rdf in Excel and do the
integration, I get N=1. 

 

I should add that I have seen from the manual that the “-surf”
option means that normalization cannot be used. Hence, in my calculations I do
not normalize the integral with V/N.

 

Does anyone have any suggestions?

 

Best regards,

Soren







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[gmx-users] topology file for two molecules

[Gavin Melaugh]

Hi all

I want to run a simulation of one tert-pentane molecule inside one
organic cage molecule. I have the topology files for both molecules but
obviously I only need one .top file as the input for grompp. What is the
most convenient way of having both topologies in one file?

Many Thanks

Gavin
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[gmx-users] g_rdf normalization

[Enemark Soeren]

Dear fellow Gromacs users
Does anyone know how the "-surf mol" option works?

I am trying to calculate the coordination number for a molecule in a slice 
(xy-plane, delta-z ~ 0.5 nm) of my system. I believe I understand how to do the 
integration of the RDF function if I use the center-of-mass option (-rdf 
mol_com), but I am more interested in calculating the coordination number with 
respect to the molecular surface. I have tried to use the "-surf mol" option 
together with "-cn ", and I get what I expected to get, namely N=2. However, 
when I import the rdf in Excel and do the integration, I get N=1.

I should add that I have seen from the manual that the "-surf" option means 
that normalization cannot be used. Hence, in my calculations I do not normalize 
the integral with V/N.

Does anyone have any suggestions?

Best regards,
Soren
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RE: [gmx-users] MPI and dual-core laptop

[Berk Hess]

Hi,

You don't need MPI within one machine.
Gromacs 4.5 has a built in thread-mpi library that gets built automatically.

Berk

> Date: Tue, 28 Sep 2010 10:22:30 +0200
> From: domm...@icp.uni-stuttgart.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] MPI and dual-core laptop
> 
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> On 09/27/2010 08:42 PM, simon sham wrote:
> > Hi,
> > I wanted to test the GROMACS MPI version in my dual-processors laptop. I
> > have installed openmpi 1.4.2 version. However, when I tried to configure
> > GROMACS 4.5.1 with --enable-mpi option, I got the following
> > configuration problem:
> > 
> > "checking whether the MPI cc command works... configure: error: Cannot
> > compile and link MPI code with mpicc"
> > 
> > 
> > mpicc is in my /usr/local/bin directory.
> > 
> > Questions:
> > 1. Can I run GROMACS 4.5.1 in a dual-processor laptop?
> > 2. If yes, how should I configure the software?
> > 
> > Thanks in advance for your insight.
> > 
> > Best,
> > 
> > Simon Sham
> > 
> > 
> 
> Hi,
> 
>  it seems the mpicc compiler does not find the necessary libraries to
> link or doesn't even find the compiler. Check if mpicc is in your path.
> 
> To include the missing libraries in the GROMACS configuration use the
> LDFLAGS and CPPFLAGS variables to set the corresponding pathes.
> 
> CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure ...
> 
> If you have to add further include and library directories you have to
> add a further -I/... and/or -L/... and put the whole expression after
> the = into quotes, e.g CPPFLAGS="-I/usr/local/lib
> - -I/home/user/local/fftw3/include" and so on.
> 
> However if you use Gromacs 4.5 I would use and get common with the CMake
> system, which really works fine and also a GUI is available that allows
> you to easy set your variables options.
> 
> /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
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.10 (GNU/Linux)
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> 
> iEYEARECAAYFAkyhpcYACgkQLpNNBb9GiPm1AgCfWcXsF7zs+fGV2gGFiGgG1H4o
> tC0AoJRxehKCtgYNSq8qa5fqbEagde8a
> =YCG5
> -END PGP SIGNATURE-
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Re: [gmx-users] Reg: Liquid-liquid interface simulation

[David van der Spoel]

On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote:

Hi all

Is that any one have liquid-liquid interface simulation (like lysozyme
by justin). if so kindly share it through this discussiion forum.it
 will be of great help for the newusers like me to use
gromacs for liquid-liquid interface simulation.

Regards
Vinoth

We prefer to keep discussions on the mailing list for more direct impact 
and for archiving purposes. If there are tutorials or howtos on certain 
topics they can be uploaded to the website.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] MPI and dual-core laptop

[Florian Dommert]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 09/27/2010 08:42 PM, simon sham wrote:
> Hi,
> I wanted to test the GROMACS MPI version in my dual-processors laptop. I
> have installed openmpi 1.4.2 version. However, when I tried to configure
> GROMACS 4.5.1 with --enable-mpi option, I got the following
> configuration problem:
> 
> "checking whether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with mpicc"
> 
> 
> mpicc is in my /usr/local/bin directory.
> 
> Questions:
> 1. Can I run GROMACS 4.5.1 in a dual-processor laptop?
> 2. If yes, how should I configure the software?
> 
> Thanks in advance for your insight.
> 
> Best,
> 
> Simon Sham
> 
> 

Hi,

 it seems the mpicc compiler does not find the necessary libraries to
link or doesn't even find the compiler. Check if mpicc is in your path.

To include the missing libraries in the GROMACS configuration use the
LDFLAGS and CPPFLAGS variables to set the corresponding pathes.

CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure ...

If you have to add further include and library directories you have to
add a further -I/... and/or -L/... and put the whole expression after
the = into quotes, e.g CPPFLAGS="-I/usr/local/lib
- -I/home/user/local/fftw3/include" and so on.

However if you use Gromacs 4.5 I would use and get common with the CMake
system, which really works fine and also a GUI is available that allows
you to easy set your variables options.

/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] Reg: Liquid-liquid interface simulation

[vinothkumar mohanakrishnan]

Hi all

Is that any one have liquid-liquid interface simulation (like lysozyme by
justin). if so kindly share it through this discussiion forum.it will be of
great help for the newusers like me to use gromacs for liquid-liquid
interface simulation.

Regards
Vinoth
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Re: [gmx-users] My FEP so far (1)

[Sander Pronk]

Hi,

The procedure you're describing is correct (and I believe g_analyze can do the 
integration for you). However, with 4.5 there's a new way to calculate free 
energies, using Bennett' s Acceptance Ratio. 

That method relies on the energy differences between the state the simulation 
is at (init_lambda in this case) and the state you want to calculate the free 
energy difference for, as a set of instantaneous values, written to 'dhdl.xvg'. 
You can enable calculating the energies w.r.t.  those states with the 'foreign 
lambda' mdp parameter. For example, if you'd like 6 lambda points between 0 and 
1, your mdp parameters would look like this:

init_lambda foreign_lambda
0.00.2
0.2 0.0 0.4
0.4 0.2 0.6
0.6 0.4 0.8
0.8 0.6 1.0
1.0 0.8

(so for each simulation at a specific lambda point there are two foreign 
lambdas, one with the 'previous' lambda value and one with the 'next' lambda 
value). BTW, 6 lambda points is probably not enough.

You could also set all foreign_lambda values to all lambda values you're 
simulating at: '0.0 0.2 0.4 0.6 0.8 1.0' for all simulations - the method would 
work but you'll lose some disk space (and maybe some performance when there are 
a lot of lambda points). 

You can then use g_bar to calculate the full free energy difference with error 
estimates (for example, g_bar -f lambda=*/dhdl.xvg) . This method has much 
better statistical (and numerical) properties than integrating dH/dl.

I hope all this makes sense. We're working on getting an updated free energy 
tutorial - I'll announce it here when we're done.

Sander


On Sep 28, 2010, at 02:47 , TJ Mustard wrote:

> Hello all,
>  
> As there is very little out on the web for FEP in gromacs that is up to date 
> I thought I would throw my two cents out there for approval of my techniques 
> (hopefully) and to help others that find this subject hard to get a 
> significant amount of information on. Of course there are papers to be read 
> but the specific settings and how to go about them are
>  
> First if you are using 4.5+ I found that it has arguments that can be set in 
> its mdp files:
>  
> ; Free energy control stuff
> free-energy  = yes  ; = no
> init-lambda  = 0.00 ; = 0
> delta-lambda = 0; = 0
> foreign_lambda   =  ; =
> sc-alpha = 0.5  ; = 0
> sc-power = 1.0  ; = 0
> sc-sigma = 0.3  ; = 0.3
> nstdhdl  = 10   ; = 10
> separate-dhdl-file   = yes  ; = yes
> dhdl-derivatives = yes  ; = yes
> dh_hist_size = 0; = 0
> dh_hist_spacing  = 0.1  ; = 0.1
> couple-moltype   = RNA_chain_A  ; =
> couple-lambda0   = vdw-q; = vdw-q
> couple-lambda1   = none ; = vdw-q
> couple-intramol  = no   ;   = no
>  
>  
> On this run I set the RNA_chain_A to be perturbation. I also set the change 
> to be all interactions to none. To keep artifacts to a minimum I set the "sc" 
> settings as above. (found these in the FEP tutorial online here 
> http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) I 
> would then make several identical runs with different init_lambda values. The 
> md or sd log file would output the average dVpot/dLambda and I would put 
> these values in a spreadsheet vs their respective lambda values. I would then 
> use Simpson's Rule or other to approximate the area under the curve. With 
> this technique and lambda steps of 0.05 I calculated the FEP for the 
> hydration of methane to be ~2.5 kcal/mol. Not perfect but in the ballpark 
> according to the tutorial above.
>  
> I found that the addition of this argument set in 4.5+ allowed for easier 
> FEP. (ie not having to manually edit the state b for each atom in question.)
>  
> If anyone else has anything so add or correct please do so. I found this very 
> difficult to understand as the tutorial is for a different force field and my 
> future systems were going to be much larger.
>  
> Thank you,
>  
> TJ Mustard
> Email: musta...@onid.orst.edu
> 
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Re: [gmx-users] MPI and dual-core laptop

[Carsten Kutzner]

Hi,

if you only want to use the two processors of you laptop you
can simple leave away the --enable-mpi flag. Then it will
work in parallel using threads. Use mdrun -nt 2 -s ...
to specify two threads.

If you anyhow want to compile with MPI, take a look
at the config.log file (search for 'Cannot compile and link MPI code')
to check the actual cause of your problem,
probably some library was not found.

Carsten


On Sep 27, 2010, at 8:42 PM, simon sham wrote:

> Hi,
> I wanted to test the GROMACS MPI version in my dual-processors laptop. I have 
> installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 
> 4.5.1 with --enable-mpi option, I got the following configuration problem:
> 
> "checking whether the MPI cc command works... configure: error: Cannot 
> compile and link MPI code with mpicc"
> 
> 
> mpicc is in my /usr/local/bin directory.
> 
> Questions:
> 1. Can I run GROMACS 4.5.1 in a dual-processor laptop?
> 2. If yes, how should I configure the software?
> 
> Thanks in advance for your insight.
> 
> Best,
> 
> Simon Sham
> 
> -- 
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--
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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[gmx-users] compiling gromacs4.5 with gpu

[BIN ZHANG]

Hi, there:

I was trying to compile gromacs4.5.1 on a GPU cluster (https://secure.nersc.gov/nusers/systems/dirac/ 
).


The compilation seems to work fine, but in the installation folder,  
only "bin/mdrun-gpu" presents. Is it supposed to be so?


When I type "./mdrun-gpu -h", the following error occurs:
./mdrun-gpu: error while loading shared libraries: libgmxpreprocess.so. 
6: cannot open shared object file: No such file or directory


Do you have any idea what this means?

Thanks a lot,
Bin

=
Here are steps I did for compiling:
export OPENMM_ROOT_DIR=/global/homes/b/bingo/Program/OpenMM2.0-Linux64
cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=/global/homes/b/bingo/ 
Program/gromacs_gpu

make mdrun
make install-mdrun

==
Here are the outputs from the cmake

-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- CTest cannot determine repository type. Please set UPDATE_TYPE to  
'cvs' or 'svn'. CTest update will not work.

-- Performing Test CFLAGS_WARN
-- Performing Test CFLAGS_WARN - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Failed
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Failed
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- No external FFT libraries needed for the OpenMM build, using fftpack!
-- Threads not compatible with OpenMM build, disabled!
CMake Warning at CMakeLists.txt:183 (message):
  CPU-based acceleration turned off, OpenMM does not support/need any!


-- Looking for include files HAVE_STRING_H
-- Looking for include files HAVE_STRING_H - found
-- Looking for include files HAVE_MATH_H
-- Looking for include files HAVE_MATH_H - found
-- Looking for include files HAVE_LIMITS_H
-- Looking for include files HAVE_LIMITS_H - found
-- Looking for include files HAVE_MEMORY_H
-- Looking for include files HAVE_MEMORY_H - found
-- Looking for include files HAVE_UNISTD_H
-- Looking for include files HAVE_UNISTD_H - found
-- Looking for include files HAVE_PWD_H
-- Looking for include files HAVE_PWD_H - found
-- Looking for include files HAVE_STDINT_H
-- Looking for include files HAVE_STDINT_H - found
-- Looking for include files HAVE_STDLIB_H
-- Looking for include files HAVE_STDLIB_H - found
-- Looking for include files HAVE_PTHREAD_H
-- Looking for include files HAVE_PTHREAD_H - found
-- Looking for include files HAVE_DIRENT_H
-- Looking for include files HAVE_DIRENT_H - found
-- Looking for include files HAVE_INTTYPES_H
-- Looking for include files HAVE_INTTYPES_H - found
-- Looking for include files HAVE_REGEX_H
-- Looking for include files HAVE_REGEX_H - found
-- Looking for include files HAVE_SYS_TYPES_H
-- Looking for include files HAVE_SYS_TYPES_H - found
-- Looking for include files HAVE_SYS_STAT_H
-- Looking for include files HAVE_SYS_STAT_H - found
-- Looking for include files HAVE_SYS_TIME_H
-- Looking for include files HAVE_SYS_TIME_H - found
-- Looking for include files HAVE_RPC_RPC_H
-- Looking for include files HAVE_RPC_RPC_H - found
-- Looking for include files HAVE_RPC_XDR_H
-- Looking for include files HAVE_RPC_XDR_H - found
-- Looking for include files HAVE_XMMINTRIN_H
-- Looking for include files HAVE_XMMINTRIN_H - found
-- Looking for include files HAVE_EMMINTRIN_H
-- Looking for include files HAVE_EMMINTRIN_H - found
-- Looking for include files HAVE_PMMINTRIN_H
-- Looking for include files HAVE_PMMINTRIN_H - not found.
-- Looking for include files HAVE_SMMINTRIN_H
-- Looking for include files HAVE_SMMINTRIN_H - not found.
-- Looking for include files HAVE_IO_H
-- Looking for include files HAVE_IO_H - not found.
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strdup
-- Looking for strdup - found
-- Looking for vprintf
-- Looking for vprintf - found
-- Looking for memcmp
-- Looking for memcmp - found
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - found
-- Looking for _aligned_malloc
-- Looking for _aligned_malloc - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for isnan
-- Looking for isnan - found
-- Looking for _isnan
-- Looking for _isnan - not found
-- Looking for isfinite