RE: [gmx-users] how to let the grompp finding library fromworkingdirectory first.

[#ZHAO LINA#]

The HO.itp is nothing wrong with this.

I found the answer from last part of this page 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html).

It's a bit trivial and I will test it later.

Thanks again for you time.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 1:35 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library 
fromworkingdirectory first.

What is the contents of the HO.itp file?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:53 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library 
fromworkingdirectory first.

Yes.

I did it already. But it did not work.
in topol.top file,
;Include topology
#include "HO.itp"

Thanks,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 12:48 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library from 
workingdirectory first.
What is the contents of your topol.top and HO.itp file?  Does the topol.top 
“include” the HO.itp in it?

To have an “included topology file” (.itp) file processed by grompp, it has to 
be directed to it.  This is typically done by using a #include “HO.itp” line 
within the topol.top file.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to let the grompp finding library from 
workingdirectory first.

Hi,

The HO atom type was in the working directory .itp file.
How can I let the grompp work from searching the library of the working 
directory, not like this:

grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr


checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I do not 
realise.

Thanks and best regards,

lina
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RE: [gmx-users] how to let the grompp finding library fromworkingdirectory first.

[Dallas Warren]

What is the contents of the HO.itp file?

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:53 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library
fromworkingdirectory first.

 

Yes.  

I did it already. But it did not work.
in topol.top file,
;Include topology
#include "HO.itp"

Thanks,

lina



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 12:48 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library from
workingdirectory first.

What is the contents of your topol.top and HO.itp file?  Does the
topol.top "include" the HO.itp in it?

 

To have an "included topology file" (.itp) file processed by grompp, it
has to be directed to it.  This is typically done by using a #include
"HO.itp" line within the topol.top file.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to let the grompp finding library from
workingdirectory first.

 

Hi,

The HO atom type was in the working directory .itp file.
How can I let the grompp work from searching the library of the working
directory, not like this:

grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr


checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I
do not realise.

Thanks and best regards,

lina

-- 
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Re: [gmx-users] Correction for the PBC!

[teklebrh]

Dear Justine,

I just checked at the archive list and found out lots of information  
on how to correct for PBC! And if I understood it correctly is this  
the right way to follow...

“If you are trying to correct for periodicity for all species in the system
(protein and water) then a few iterations of trjconv may be necessary, i.e.
-center (on protein), followed by -pbc nojump or -pbc mol -ur compact.  Using
trjconv is a bit hit-or-miss, and just requires a bit of playing to  
get things working how you want them.”


trjconv –f xxx.xtc –o x_cluster.gro –b 19000 –e 2 –pbc cluster

grompp –f xx.mdp –c x_cluster.gro –o x_cluster.tpr

trjconv –f xxx.xtc –o x_cluster.xtc –b 19000 –e 2 –s  
xx_cluster.tpr –pbc nojump


Then I have to do anaysis on the new .tpr and .xtc.. is that correct

Is this the right way to correct for periodicity... I took the idea  
from you and Chris. I have done the RDF and distance measurement but  
looks a bit off my RDF did not converge to 1. They recommend me to do  
PBC correction on my system which is run for 20ns. I am doing the  
analysis on the last 1ns (from 19-20 ns)


You suggestion is always helpful!

Rob







Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Dear Gromacs,

I want to correct the periodic boundry condition before analyzing  
my data, how do I perform that?




Please see trjconv -h, as well as any of the thousands of posts in  
the list archive related to this topic.


-Justin


any suggest!

Rob


--


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] how to let the grompp finding library from workingdirectory first.

[#ZHAO LINA#]

Yes.

I did it already. But it did not work.
in topol.top file,
;Include topology
#include "HO.itp"

Thanks,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 12:48 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library from 
workingdirectory first.

What is the contents of your topol.top and HO.itp file?  Does the topol.top 
“include” the HO.itp in it?

To have an “included topology file” (.itp) file processed by grompp, it has to 
be directed to it.  This is typically done by using a #include “HO.itp” line 
within the topol.top file.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to let the grompp finding library from 
workingdirectory first.

Hi,

The HO atom type was in the working directory .itp file.
How can I let the grompp work from searching the library of the working 
directory, not like this:

grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr


checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I do not 
realise.

Thanks and best regards,

lina
-- 
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RE: [gmx-users] how to let the grompp finding library from workingdirectory first.

[Dallas Warren]

What is the contents of your topol.top and HO.itp file?  Does the
topol.top "include" the HO.itp in it?

 

To have an "included topology file" (.itp) file processed by grompp, it
has to be directed to it.  This is typically done by using a #include
"HO.itp" line within the topol.top file.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to let the grompp finding library from
workingdirectory first.

 

Hi,

The HO atom type was in the working directory .itp file.
How can I let the grompp work from searching the library of the working
directory, not like this:

grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr


checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I
do not realise.

Thanks and best regards,

lina

-- 
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[gmx-users] how to let the grompp finding library from working directory first.

[#ZHAO LINA#]

Hi,

The HO atom type was in the working directory .itp file.
How can I let the grompp work from searching the library of the working 
directory, not like this:

grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr


checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I do not 
realise.

Thanks and best regards,

lina
-- 
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Re: [gmx-users] atom type parameters

[Mark Abraham]

- Original Message -
From: Ramachandran G 
Date: Tuesday, September 14, 2010 12:39
Subject: [gmx-users] atom type parameters
To: gmx-users@gromacs.org

> Dear gmx-users:
> I am trying to get the topology for a chromophore exist in the Green 
> fluoresent protein.  Although to some extent i got success in building the 
> parameters in the 'ff*.rtp' file,
> i got struck in building 'atom type parameter' ( ff*.atp). I am trying to use 
> Charmm force field. Can anyone help me. Thank you.

 Your request is a bit open-ended... You will need a thorough knowledge of 
chapter 5 of the manual. People may be able to help you if you show what you 
did, explain what you wanted and why you think it didn't work.

Mark

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[gmx-users] atom type parameters

[Ramachandran G]

Dear gmx-users:
I am trying to get the topology for a chromophore exist in the Green
fluoresent protein.  Although to some extent i got success in building the
parameters in the 'ff*.rtp' file,
i got struck in building 'atom type parameter' ( ff*.atp). I am trying to
use Charmm force field. Can anyone help me. Thank you.


with regards,
Rama
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Re: [gmx-users] FEP top file setup...

[Mark Abraham]

- Original Message -
From: TJ Mustard 
Date: Tuesday, September 14, 2010 10:54
Subject: [gmx-users] FEP top file setup...
To: "gmx-users@gromacs.org" 

  
---
| 

 
> I am tryng to run free energy perturbation (FEP) calculations on several 
> ligands in several proteins. My problem is getting the correct B state atoms 
> and charges for AMBER forcefields. If anyone can point me in the correct 
> direction, that would be great.
   
  I have read the Free Energy Tutorial from the Dill group wiki and found 
it very informative on how I should set up the top file and the experiment as a 
whole. But I can't seem to get the jobs to run correctly. I am assuming that 
the top file is incorrectly setup as the jobs run with lambda = 0.
 |
---

It sounds to me more like your  .mdp might be wrong. Check out the FE section 
of manual 7.3

Mark



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[gmx-users] FEP top file setup...

[TJ Mustard]

  

  
I am tryng to run free energy perturbation (FEP) calculations on several ligands in several proteins. My problem is getting the correct B state atoms and charges for AMBER forcefields. If anyone can point me in the correct direction, that would be great.

 

I have read the Free Energy Tutorial from the Dill group wiki and found it very informative on how I should set up the top file and the experiment as a whole. But I can't seem to get the jobs to run correctly. I am assuming that the top file is incorrectly setup as the jobs run with lambda = 0.

 

Thank you in advance,

 

TJ Mustard
Email: musta...@onid.orst.edu
  

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RE: [gmx-users] Gibbs Energy Calculation, Water/Octanol Partioning

[Dallas Warren]

FYI, the sd versus md is stable and our runs are now completing fully and we 
are obtaining the correct Gibbs energy values.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Dallas Warren
> Sent: Wednesday, 8 September 2010 3:41 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] Gibbs Energy Calculation, Water/Octanol
> Partioning
> 
> Justin,
> 
> > Have you tried using the sd integrator?  That's what the authors of
> this paper
> > used.  I don't know if there are stability issues with md vs. sd, but
> it's a
> > starting point.
> 
> That does appear to be the issue.  We have repeated the pentane in
> octanol lambda runs and it completed without any errors.  Going back
> now to repeat a few other things, and will report back once have
> checked everything out.
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Medicinal Chemistry and Drug Action
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
> +61 3 9909 9304
> -
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
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[gmx-users] implicit solvent and counter ions

[Schor, Marieke]

As gromacs 4.5 doesn't use a saltconcentration for implicit solvent 
calculations I was wondering what to do with a charged protein. Should I add 
counterions or not? 

Thanks,
Marieke
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Re: [gmx-users] Coorection for the PBC!

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:

Dear Gromacs,

I want to correct the periodic boundry condition before analyzing my 
data, how do I perform that?




Please see trjconv -h, as well as any of the thousands of posts in the list 
archive related to this topic.


-Justin


any suggest!

Rob


--


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] Coorection for the PBC!

[teklebrh]

Dear Gromacs,

I want to correct the periodic boundry condition before analyzing my  
data, how do I perform that?


any suggest!

Rob
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RE: [gmx-users] problem with .edr file

[Berk Hess]

Hi,

There is no problem at all and you only got notices, not errors.
In Gromacs version 4.0 and before each frame in an energy file always contained 
the energy averages
over the whole simulation up to the current step. For proper checkpointing we 
therefore had to write
an energy energy file frame every time a checkpoint is written. The frames 
cause no problems and all,
and g_energy ignores them by default.

Starting with version 4.5 energy frames only contain the average starting from 
the time when the previous
frame was written and we could get rid of the inelegant (bug harmless) extra 
frames.

Note that the energy file that you obtained from the rerun does not have the 
exact averages and fluctuations
with statistics over all md steps.

Berk

Date: Mon, 13 Sep 2010 09:59:43 +0200
From: anna.marabo...@isa.cnr.it
To: gmx-users@gromacs.org
Subject: [gmx-users] problem with .edr file








Dear 
gmx-users,
I launched several 
dynamics with gromacs 4.0.7, they finished regularly with apparently no 
problems 
(=no error messages at the end of the runs), but when I started analyzing the 
results, I found a problem in the .edr files. In details, when I used them with 
g_energy, I found that only 4 of the points that should have been saved as I 
stated in the .mdp file ( I set to save energy, force, coordinates, log every 
100 ps) were present in the file. The .log files were correct and I can see 
energies in all the steps. I checked both the .trr and the .edr files with 
gmxcheck and I found that the .trr (and also the .xtc) files were correct, 
whereas the .edr files gave me the following message error:
 
Checking energy file 
FAPP2-GLTPapo_md20ns1.edr
 
Opened FAPP2-GLTPapo_md20ns1.edr as single 
precision energy file
frame:  6 (index  
0), t:120.000
Reading energy 
frame  2 time  300.000
Timesteps at t=200 
don't match (80, 100)
Reading energy frame200 time 
20100.000
Timesteps at t=20100 don't match (100, 20)
Last energy frame 
read 201 time 20120.000
 
Found 202 frames.
 
I used mdrun -rerun 
and the .trr file to obtain a new .edr file, and this time the file was 
correct, 
with all the points present, so I think that the run was made correctly, but 
the 
.edr was not properly saved. I don't know why this happened: do you think it 
could be a problem in the Gromacs version, or in the Gromacs installation? Any 
hint will be very appreciated.
Many thanks in 
advance and best regards
Anna

Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and 
Computational Biology
Institute of Food Science, 
CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabo...@isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"If you think you are too small to make 
a difference, try sleeping with a mosquito"
 

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Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

[Alan]

Dear Rossen,

Thanks for your reply.

For your info I use Mac 10.6 with Fink in 64 bits. I have access to svn
Openmm dev source code so I am compiling it in 64 bits. It could be a source
of issues, but all others programmes I have running that depends on openmm
(e.g. sander_openmm) were working fine except GMX.

Bizzarely but gmx 4.5 beta were compiling ok.

I will try release-4-5-patches updated later.

Thanks,

Alan

On 13 September 2010 12:58, Rossen Apostolov  wrote:

>  Just to add: the pre-built OpenMM-2.0 for Mac are compiled for 32bit. If
> you get an error as:
>
> Linking CXX shared library libopenmm_api_wrapper.dylib
> ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for
> i386 which is not the architecture being linked (x86_64)
> Undefined symbols:
>   "OpenMM::State::getVelocities() const", referenced from:
>  snip .
>
> then you can force compilation for 32bit by:
>
> $ export CFLAGS='-arch i386'
> $ export CXXFLAGS='-arch i386'
>
> or recompile the openmm from source.
>
> Rossen
>
>
> On 9/13/10 1:01 PM, Rossen Apostolov wrote:
>
> Hi Alan,
>
> There was a missing dependency for building gmx_gpu_utils, but for some
> reason compilation didn't break on linux:) This is now fixed in
> release-4-5-patches. Pay attention though that the prebuilt  OpenMM-2.0
> libraries from the SimTK website are for MacOSX 10.6
>
> Rossen
>
> On 9/11/10 12:56 AM, Alan wrote:
>
> I am doing, after compiling and installing the normal grmx 4.5:
>
>  rm -fr CMakeCache.txt
> make clean
> export OPENMM_ROOT_DIR=/usr/local/openmm
>  cmake -DGMX_OPENMM=ON ..
> make mdrun
>  [  1%] Building NVCC (Device) object
> src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
> [  1%] Building NVCC (Device) object
> src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
> Scanning dependencies of target gmx_gpu_utils
> Linking CXX shared library libgmx_gpu_utils.dylib
> Undefined symbols:
>   "_gmx_strncasecmp", referenced from:
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   "_debug", referenced from:
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   do_timed_memtest(int, int)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   do_full_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   do_quick_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   "_trim", referenced from:
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
> make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all]
> Error 2
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
> make: *** [mdrun] Error 2
>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <<
>
>
>
> --
> -Rossen
>
>
>
> --
> -Rossen
>
>
> --
> 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
>



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

Re: [gmx-users] Re: Reg: Gromacs binary liquid-liquid simulation

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:
hi i have 20 coordinates in the .gro file from PRODRG server where as i 
have only 6 atom coordidates in the .top file this file also i got from 
PRODRG. below i am giving both my .top file as well as .gro file for 
hexane. do i manually edit the .top file from PRODRG to match the 
coordinates, if so how?.my worry again is when i give this command




You're trying to use an all-atom coordinate file with a united-atom force field. 
 Do not try to add atoms to the topology.  Use an appropriate coordinate file.


Also, the charges assigned to the hexane molecule (like much of the output from 
PRODRG) are probably not correct.  In UA force fields like Gromos, aliphatic 
groups should be uncharged.  Note that there is a charge imbalance in your 
molecule, such that there is a permanent, albeit small, net dipole on the 
molecule.  Ask yourself: does this model reflect reality?


genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o 
hexane_multi.gro -nmol 100 -seed 1997


the .top file doesn't get updated with more number (say 101) of hexane 
molecules in the molecules section.kindly advice me on this point.




Perhaps the box you're using simply can't fit more than 101 molecules.

-Justin


hexane.top

#include "ffG43a1.itp"

[ moleculetype ]
; Name nrexcl
hexane  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1   CH3 1  DRG CAA 1   -0.018  15.0350  
 2   CH2 1  DRG CAB 10.011  14.0270  
 3   CH2 1  DRG CAC 10.008  14.0270  
 4   CH2 1  DRG CAD 10.009  14.0270  
 5   CH2 1  DRG CAE 10.009  14.0270  
 6   CH3 1  DRG CAF 1   -0.019  15.0350  


[ bonds ]
; ai  aj  fuc0, c1, ...
   2   1   20.153   715.00.153   715.0 ;   CAB  CAA  
   2   3   20.153   715.00.153   715.0 ;   CAB  CAC  
   3   4   20.153   715.00.153   715.0 ;   CAC  CAD  
   4   5   20.153   715.00.153   715.0 ;   CAD  CAE  
   5   6   20.153   715.00.153   715.0 ;   CAE  CAF  


[ pairs ]
; ai  aj  fuc0, c1, ...
   1   4   1   ;   CAA  CAD  
   2   5   1   ;   CAB  CAE  
   3   6   1   ;   CAC  CAF  


[ angles ]
; ai  aj  ak  fuc0, c1, ...
   1   2   3   2109.5   520.0109.5   520.0 ;   CAA  CAB  
CAC  
   2   3   4   2109.5   520.0109.5   520.0 ;   CAB  CAC  
CAD  
   3   4   5   2109.5   520.0109.5   520.0 ;   CAC  CAD  
CAE  
   4   5   6   2109.5   520.0109.5   520.0 ;   CAD  CAE  
CAF  


[ dihedrals ]
; ai  aj  ak  al  fuc0, c1, m, ...
   4   3   2   1   1  0.05.9 3  0.05.9 3 ; dih   CAD  
CAC  CAB  CAA  
   5   4   3   2   1  0.05.9 3  0.05.9 3 ; dih   CAE  
CAD  CAC  CAB  
   6   5   4   3   1  0.05.9 3  0.05.9 3 ; dih   CAF  
CAE  CAD  CAC


; Include SPC water topology
#include "spc.itp"

[ system ]
hexane in water

[ molecules ]
;molecule name number
hexane 101
SOL  1764

hexane.gro
PRODRG COORDS
   20
1DRG  CAA  1   0.684  -0.063   1.332
1DRG  HAA  2   0.684   0.013   1.254
1DRG  HAB  3   0.583  -0.075   1.371
1DRG  HAC  4   0.724  -0.158   1.295
1DRG  CAB  5   0.778  -0.021   1.445
1DRG  HAD  6   0.776  -0.098   1.522
1DRG  HAE  7   0.744   0.077   1.479
1DRG  CAC  8   0.923  -0.003   1.396
1DRG  HAF  9   0.950  -0.087   1.332
1DRG  HAG 10   0.985   0.007   1.485
1DRG  CAD 11   0.940   0.127   1.316
1DRG  HAH 12   0.913   0.211   1.380
1DRG  HAI 13   0.878   0.117   1.227
1DRG  CAE 14   1.085   0.145   1.267
1DRG  HAJ 15   1.087   0.222   1.190
1DRG  HAK 16   1.118   0.047   1.232
1DRG  CAF 17   1.179   0.186   1.380
1DRG  HAM 18   1.149   0.284   1.418
1DRG  HAN 19   1.281   0.191   1.342
1DRG  HAL 20   1.168   0.108   1.456
   0.84818   0.84818   0.84818

Regards
Vinoth 

On Mon, Sep 13, 2010 at 4:26 PM, Justin A. Lemkul > wrote:




vinothkumar mohanakrishnan wrote:

i want to do MD for hexane-water system. I got hexane.gro and
hexane..itp from PRODRG 2.5 Beta server with that i made the
hexane.top file. below is the serious of commands i executed in
gromacs, i am adding 200 hexane molecules an 1115 water
molecules. after the first genbox i checked my topolgy file
wheather the no .of hexane molecules got updated r increased to
200 but it doesn't and remains as 1 and then i maually changed
it to 200 in the molecules section. i dont know where


Per your genbox command below, if you have one hexane (in
hexane_box.gro) and you a

Re: [gmx-users] Re: Reg: Gromacs binary liquid-liquid simulation

[vinothkumar mohanakrishnan]

hi i have 20 coordinates in the .gro file from PRODRG server where as i have
only 6 atom coordidates in the .top file this file also i got from PRODRG.
below i am giving both my .top file as well as .gro file for hexane. do i
manually edit the .top file from PRODRG to match the coordinates, if so
how?.my worry again is when i give this command

genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o
hexane_multi.gro -nmol 100 -seed 1997

the .top file doesn't get updated with more number (say 101) of hexane
molecules in the molecules section.kindly advice me on this point.

hexane.top

#include "ffG43a1.itp"

[ moleculetype ]
; Name nrexcl
hexane  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1   CH3 1  DRG CAA 1   -0.018  15.0350
 2   CH2 1  DRG CAB 10.011  14.0270
 3   CH2 1  DRG CAC 10.008  14.0270
 4   CH2 1  DRG CAD 10.009  14.0270
 5   CH2 1  DRG CAE 10.009  14.0270
 6   CH3 1  DRG CAF 1   -0.019  15.0350

[ bonds ]
; ai  aj  fuc0, c1, ...
   2   1   20.153   715.00.153   715.0 ;   CAB  CAA
   2   3   20.153   715.00.153   715.0 ;   CAB  CAC
   3   4   20.153   715.00.153   715.0 ;   CAC  CAD
   4   5   20.153   715.00.153   715.0 ;   CAD  CAE
   5   6   20.153   715.00.153   715.0 ;   CAE  CAF

[ pairs ]
; ai  aj  fuc0, c1, ...
   1   4   1   ;   CAA  CAD
   2   5   1   ;   CAB  CAE
   3   6   1   ;   CAC  CAF

[ angles ]
; ai  aj  ak  fuc0, c1, ...
   1   2   3   2109.5   520.0109.5   520.0 ;   CAA  CAB
CAC
   2   3   4   2109.5   520.0109.5   520.0 ;   CAB  CAC
CAD
   3   4   5   2109.5   520.0109.5   520.0 ;   CAC  CAD
CAE
   4   5   6   2109.5   520.0109.5   520.0 ;   CAD  CAE
CAF

[ dihedrals ]
; ai  aj  ak  al  fuc0, c1, m, ...
   4   3   2   1   1  0.05.9 3  0.05.9 3 ; dih   CAD  CAC
CAB  CAA
   5   4   3   2   1  0.05.9 3  0.05.9 3 ; dih   CAE  CAD
CAC  CAB
   6   5   4   3   1  0.05.9 3  0.05.9 3 ; dih   CAF  CAE
CAD  CAC

; Include SPC water topology
#include "spc.itp"

[ system ]
hexane in water

[ molecules ]
;molecule name number
hexane 101
SOL  1764

hexane.gro
PRODRG COORDS
   20
1DRG  CAA  1   0.684  -0.063   1.332
1DRG  HAA  2   0.684   0.013   1.254
1DRG  HAB  3   0.583  -0.075   1.371
1DRG  HAC  4   0.724  -0.158   1.295
1DRG  CAB  5   0.778  -0.021   1.445
1DRG  HAD  6   0.776  -0.098   1.522
1DRG  HAE  7   0.744   0.077   1.479
1DRG  CAC  8   0.923  -0.003   1.396
1DRG  HAF  9   0.950  -0.087   1.332
1DRG  HAG 10   0.985   0.007   1.485
1DRG  CAD 11   0.940   0.127   1.316
1DRG  HAH 12   0.913   0.211   1.380
1DRG  HAI 13   0.878   0.117   1.227
1DRG  CAE 14   1.085   0.145   1.267
1DRG  HAJ 15   1.087   0.222   1.190
1DRG  HAK 16   1.118   0.047   1.232
1DRG  CAF 17   1.179   0.186   1.380
1DRG  HAM 18   1.149   0.284   1.418
1DRG  HAN 19   1.281   0.191   1.342
1DRG  HAL 20   1.168   0.108   1.456
   0.84818   0.84818   0.84818

Regards
Vinoth

On Mon, Sep 13, 2010 at 4:26 PM, Justin A. Lemkul  wrote:

>
>
> vinothkumar mohanakrishnan wrote:
>
>> i want to do MD for hexane-water system. I got hexane.gro and hexane..itp
>> from PRODRG 2.5 Beta server with that i made the hexane.top file. below is
>> the serious of commands i executed in gromacs, i am adding 200 hexane
>> molecules an 1115 water molecules. after the first genbox i checked my
>> topolgy file wheather the no .of hexane molecules got updated r increased to
>> 200 but it doesn't and remains as 1 and then i maually changed it to 200 in
>> the molecules section. i dont know where
>>
>
> Per your genbox command below, if you have one hexane (in hexane_box.gro)
> and you add 200 (with -nmol), you should then have 201 hexane molecules in
> the system.
>
>
>  iam going wrong and i always get the error message as " number of
>> coordinates in coordinate file (hexane_solv.gro, 7365) does not match
>> topology (hexane.top, 4545) " while running grompp for energy minimisation.
>> i read the error gromacs (website) documentation and found that the
>> hexane.top r hexane.gro file is not getting updated, but iam helpless. any
>> help is highly appreciated. below is my topology file as well.
>>
>>
> Follow my previous advice and see if you can trace back where the error
> came from.  Count the molecules in your .gro file, i.e.:
>
> grep OW hexane_solv.gro | wc -l
>
> will give you the number of water molecules.  Do something analogous for
> hexane.  You're off 

Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

[Rossen Apostolov]

 Just to add: the pre-built OpenMM-2.0 for Mac are compiled for 32bit. 
If you get an error as:


Linking CXX shared library libopenmm_api_wrapper.dylib
ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built 
for i386 which is not the architecture being linked (x86_64)

Undefined symbols:
  "OpenMM::State::getVelocities() const", referenced from:
 snip .

then you can force compilation for 32bit by:

$ export CFLAGS='-arch i386'
$ export CXXFLAGS='-arch i386'

or recompile the openmm from source.

Rossen

On 9/13/10 1:01 PM, Rossen Apostolov wrote:

Hi Alan,

There was a missing dependency for building gmx_gpu_utils, but for 
some reason compilation didn't break on linux:) This is now fixed in 
release-4-5-patches. Pay attention though that the prebuilt  
OpenMM-2.0 libraries from the SimTK website are for MacOSX 10.6


Rossen

On 9/11/10 12:56 AM, Alan wrote:

I am doing, after compiling and installing the normal grmx 4.5:

rm -fr CMakeCache.txt
make clean
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -DGMX_OPENMM=ON ..
make mdrun
[  1%] Building NVCC (Device) object 
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
[  1%] Building NVCC (Device) object 
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

Scanning dependencies of target gmx_gpu_utils
Linking CXX shared library libgmx_gpu_utils.dylib
Undefined symbols:
  "_gmx_strncasecmp", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  "_debug", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_timed_memtest(int, int)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  do_full_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_quick_memtest(int)  in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  "_trim", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

ld: symbol(s) not found
collect2: ld returned 1 exit status
make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
make[2]: *** 
[src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2

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



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



--
-Rossen



--
-Rossen

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Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

[Rossen Apostolov]

 Hi Alan,

There was a missing dependency for building gmx_gpu_utils, but for some 
reason compilation didn't break on linux:) This is now fixed in 
release-4-5-patches. Pay attention though that the prebuilt  OpenMM-2.0 
libraries from the SimTK website are for MacOSX 10.6


Rossen

On 9/11/10 12:56 AM, Alan wrote:

I am doing, after compiling and installing the normal grmx 4.5:

rm -fr CMakeCache.txt
make clean
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -DGMX_OPENMM=ON ..
make mdrun
[  1%] Building NVCC (Device) object 
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
[  1%] Building NVCC (Device) object 
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

Scanning dependencies of target gmx_gpu_utils
Linking CXX shared library libgmx_gpu_utils.dylib
Undefined symbols:
  "_gmx_strncasecmp", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  "_debug", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_timed_memtest(int, int)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  do_full_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_quick_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  "_trim", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

ld: symbol(s) not found
collect2: ld returned 1 exit status
make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
make[2]: *** 
[src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2

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



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



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-Rossen

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[gmx-users] Re: Reg: Gromacs binary liquid-liquid simulation

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:
i want to do MD for hexane-water system. I got hexane.gro and 
hexane..itp from PRODRG 2.5 Beta server with that i made the hexane.top 
file. below is the serious of commands i executed in gromacs, i am 
adding 200 hexane molecules an 1115 water molecules. after the first 
genbox i checked my topolgy file wheather the no .of hexane molecules 
got updated r increased to 200 but it doesn't and remains as 1 and then 
i maually changed it to 200 in the molecules section. i dont know where 


Per your genbox command below, if you have one hexane (in hexane_box.gro) and 
you add 200 (with -nmol), you should then have 201 hexane molecules in the system.


iam going wrong and i always get the error message as " number of 
coordinates in coordinate file (hexane_solv.gro, 7365) does not match 
topology (hexane.top, 4545) " while running grompp for energy 
minimisation. i read the error gromacs (website) documentation and found 
that the hexane.top r hexane.gro file is not getting updated, but iam 
helpless. any help is highly appreciated. below is my topology file as well.




Follow my previous advice and see if you can trace back where the error came 
from.  Count the molecules in your .gro file, i.e.:


grep OW hexane_solv.gro | wc -l

will give you the number of water molecules.  Do something analogous for hexane. 
 You're off by 2820 atoms, which is in the ballpark of 940 waters, so something 
has broken down pretty badly somewhere.


-Justin


; The force field files to be included
#include "ffG43a1.itp"

; Include hexane topology
#include "hexane.itp"

; Include SPC water topology
#include "spc.itp"

[ system ]
hexane in Water

[ molecules ]
;molecule name number
hexane 200
SOL  1115
*
Commands*

 editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31 
3.01 3.01


genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o 
hexane_multi.gro -nmol 200 -seed 1997


genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o hexane_solv.gro

grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr

Regards
Vinoth


--


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: Gromacs binary liquid-liquid simulation

[Florian Dommert]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Check how many water atoms and hexane atoms are present in the gro file.
Then compare where differences arise. There are about 3000 atoms missing
in the top file so it seems the number of solvent or the number of
hexane molecules is wrong.

/Flo

On 09/13/2010 12:49 PM, vinothkumar mohanakrishnan wrote:
> i want to do MD for hexane-water system. I got hexane.gro and
> hexane..itp from PRODRG 2.5 Beta server with that i made the hexane.top
> file. below is the serious of commands i executed in gromacs, i am
> adding 200 hexane molecules an 1115 water molecules. after the first
> genbox i checked my topolgy file wheather the no .of hexane molecules
> got updated r increased to 200 but it doesn't and remains as 1 and then
> i maually changed it to 200 in the molecules section. i dont know where
> iam going wrong and i always get the error message as " number of
> coordinates in coordinate file (hexane_solv.gro, 7365) does not match
> topology (hexane.top, 4545) " while running grompp for energy
> minimisation. i read the error gromacs (website) documentation and found
> that the hexane.top r hexane.gro file is not getting updated, but iam
> helpless. any help is highly appreciated. below is my topology file as well.
> 
> ; The force field files to be included
> #include "ffG43a1.itp"
> 
> ; Include hexane topology
> #include "hexane.itp"
> 
> ; Include SPC water topology
> #include "spc.itp"
> 
> [ system ]
> hexane in Water
> 
> [ molecules ]
> ;molecule name number
> hexane 200
> SOL  1115
> *
> Commands*
> 
>  editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31
> 3.01 3.01
> 
> genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o
> hexane_multi.gro -nmol 200 -seed 1997
> 
> genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o hexane_solv.gro
> 
> grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr
> 
> Regards
> Vinoth
> 


- -- 
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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Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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[gmx-users] Reg: Gromacs binary liquid-liquid simulation

[vinothkumar mohanakrishnan]

i want to do MD for hexane-water system. I got hexane.gro and hexane..itp
from PRODRG 2.5 Beta server with that i made the hexane.top file. below is
the serious of commands i executed in gromacs, i am adding 200 hexane
molecules an 1115 water molecules. after the first genbox i checked my
topolgy file wheather the no .of hexane molecules got updated r increased to
200 but it doesn't and remains as 1 and then i maually changed it to 200 in
the molecules section. i dont know where iam going wrong and i always get
the error message as " number of coordinates in coordinate file
(hexane_solv.gro, 7365) does not match topology (hexane.top, 4545) " while
running grompp for energy minimisation. i read the error gromacs (website)
documentation and found that the hexane.top r hexane.gro file is not getting
updated, but iam helpless. any help is highly appreciated. below is my
topology file as well.

; The force field files to be included
#include "ffG43a1.itp"

; Include hexane topology
#include "hexane.itp"

; Include SPC water topology
#include "spc.itp"

[ system ]
hexane in Water

[ molecules ]
;molecule name number
hexane 200
SOL  1115
*
Commands*

 editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31 3.01
3.01

genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o
hexane_multi.gro -nmol 200 -seed 1997

genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o hexane_solv.gro

grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr

Regards
Vinoth
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[gmx-users] Re: Reg: Gromacs binary liquid-liquid simulation

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing the message to the list and I would ask that you 
keep all further discussion going there.


There is a mismatch between your .top and .gro, but what it is I cannot say. 
Determine how many molecules of hexane and water have been added by the commands 
you gave below; these numbers should be assigned in the [molecules] section of 
the .top file.


-Justin

vinothkumar mohanakrishnan wrote:

Dear Justin

I am vinoth currently doing my Ph.D in India (at IIT Madras). I am 
working on molecular dynamics of liqud-liquid interfaces using GROMACS 
4.0. I found in the gromacs users list that you answer many questions 
and thereby helpingg the others to find the solutions. I have certain 
doubts and i hope you will clarify that.


*My problem*: i want to do MD for hexane-water system. I got hexane.gro 
and hexane..itp from PRODRG 2.5 Beta server with that i made the 
hexane.top file. below is the serious of commands i executed in gromacs, 
and i dont know where iam going wrong and i always get the error message 
as " number of coordinates in coordinate file (hexane_solv.gro, 7365) 
does not match topology (hexane.top, 4545) " while running grompp for 
energy minimisation. i read the error gromacs (website) documentation 
and found that the hexane.top r hexane.gro file is not getting updated, 
but iam helpless. hope you will help me in finding a solution.


 editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31 
3.01 3.01


genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o 
hexane_multi.gro -nmol 200 -seed 1997


genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o hexane_solv.gro

grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr

Regards
Vinoth



--


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] RE : gmx-users Digest, Vol 77, Issue 71

[Mark Abraham]

- Original Message -
From: ABEL Stephane 175950 
Date: Monday, September 13, 2010 18:06
Subject: [gmx-users] RE : gmx-users Digest, Vol 77, Issue 71
To: gmx-users@gromacs.org

> Thank you Mark for your response
>  
> If understand well, I should only to copy these additional the 
> values in the [atomtypes] section of the ffcharmmnb.itp file 
> without others modifications/corrections. It is correct ?

No, the two styles will not co-operate, because the kind of parameters are 
fixed by the combination rule in force. You'll have to convert something by 
hand.

Mark

> > I would like to perform MD with new developped CHARMM parameters
> > in GROMACS. Since these parameters are new, they are not
> > presents in the ffcharm*.itp files  given in the of
> > charmm27.ff in the latest GMX distribution. So I have already
> > made the conversions for the bonded parameters. In case of the
> > nonbonded parameters, I have added the LJ values for the new
> > atom types at the end of the  NONBONDED section of a
> > "par_all_27_lipid.prm" file downloaded from the CHARMM website.
> > To convert the LJ values in GROMACS format, I used the perl
> > script of M. Abraham :  convert_charmm_to_gromacs.pl
> > (v.1.3) as follow :
> > 
> > perl convert_charmm_to_gromacs.pl  par_all27_lipid.prm
> > 
> > I obtain the ffcharmm.itp and ffcharmmnb.itp files as expected.
> > In the ffcharmmnb.itp the [ atomtypes ] section is present but
> > not the [ pairtypes ] section. Moreover the values in the 
> > [ atomtypes ]  are different compared to same file given in
> > latest GMX distrib (see below). Why these differences ?
> > - My ffcharmmnb.itp file
> > [ atomtypes ]
> > ;name mass charge
> > ptype 
> c6   c12
> > 
> >  CTL1 12.011000   0.0 A 
> -
> > 0.001485 -6.588e-06 ; -0.000252 -3.793e-07
> >  CTL2 12.011000   0.0 A 
> -
> > 0.001978 -4.173e-06 ; -0.000252 -3.793e-07
> >  CTL3 12.011000   0.0 A 
> -
> > 0.003011 -6.944e-06 ; -0.000252 -3.793e-07
> >  CTL5 12.011000   0.0 A 
> -
> > 0.003274 -8.007e-06 ; -0.000252 -3.793e-07
> >  CEL1 12.011000   0.0 A 
> -
> > 0.003035 -8.095e-06
> > 
> > -- GROMACS 4.5.1  ffcharmmnb.itp
> >
> > [ atomtypes ]
> > ;name at.num mass charge ptype sigma epsilon
> > 
> > CTL1 6 12.01100 0.14 A 0.405358916754 0.08368
> > CTL2 6 12.01100 0.05 A 0.358141284692 0.234304
> > CTL3 6 12.01100 -0.27 A 0.363486677001 0.326352
> > CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472
> > CEL1 6 12.01100 -0.15 A 0.372395664183 0.284512
> > .
> > Thank in advance for your halp
> 
> As the column headings note, the GROMACS 4.5 CHARMM27 uses sigma-
> epsilon VDW parameters, and my script converted to c6-c12 
> parameters. As you will see in the appropriate equations in 
> chapter 3 or 4 of the manual, such numbers will be wildly 
> different, but should produce the same energies and forces.
> 
> Mark
>  
>  > -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] RE : gmx-users Digest, Vol 77 , Issue 71

[ABEL Stephane 175950]

Thank you Mark for your response
 
If understand well, I should only to copy these additional the values in the 
[atomtypes] section of the ffcharmmnb.itp file without others 
modifications/corrections. It is correct ?
 
 Stefane

> Hi GMX users,
> 
> I would like to perform MD with new developped CHARMM parameters
> in GROMACS. Since these parameters are new, they are not
> presents in the ffcharm*.itp files  given in the of
> charmm27.ff in the latest GMX distribution. So I have already
> made the conversions for the bonded parameters. In case of the
> nonbonded parameters, I have added the LJ values for the new
> atom types at the end of the  NONBONDED section of a
> "par_all_27_lipid.prm" file downloaded from the CHARMM website.
> To convert the LJ values in GROMACS format, I used the perl
> script of M. Abraham :  convert_charmm_to_gromacs.pl
> (v.1.3) as follow :
> 
> perl convert_charmm_to_gromacs.pl  par_all27_lipid.prm
> 
> I obtain the ffcharmm.itp and ffcharmmnb.itp files as expected.
> In the ffcharmmnb.itp the [ atomtypes ] section is present but
> not the [ pairtypes ] section. Moreover the values in the 
> [ atomtypes ]  are different compared to same file given in
> latest GMX distrib (see below). Why these differences ?
> - My ffcharmmnb.itp file
> [ atomtypes ]
> ;name mass charge
> ptype c6   c12
> 
>  CTL1 12.011000   0.0 A -
> 0.001485 -6.588e-06 ; -0.000252 -3.793e-07
>  CTL2 12.011000   0.0 A -
> 0.001978 -4.173e-06 ; -0.000252 -3.793e-07
>  CTL3 12.011000   0.0 A -
> 0.003011 -6.944e-06 ; -0.000252 -3.793e-07
>  CTL5 12.011000   0.0 A -
> 0.003274 -8.007e-06 ; -0.000252 -3.793e-07
>  CEL1 12.011000   0.0 A -
> 0.003035 -8.095e-06
> 
> -- GROMACS 4.5.1  ffcharmmnb.itp
>
> [ atomtypes ]
> ;name at.num mass charge ptype sigma epsilon
> 
> CTL1 6 12.01100 0.14 A 0.405358916754 0.08368
> CTL2 6 12.01100 0.05 A 0.358141284692 0.234304
> CTL3 6 12.01100 -0.27 A 0.363486677001 0.326352
> CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472
> CEL1 6 12.01100 -0.15 A 0.372395664183 0.284512
> .
> Thank in advance for your halp

As the column headings note, the GROMACS 4.5 CHARMM27 uses sigma-epsilon VDW 
parameters, and my script converted to c6-c12 parameters. As you will see in 
the appropriate equations in chapter 3 or 4 of the manual, such numbers will be 
wildly different, but should produce the same energies and forces.

Mark
 
 
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[gmx-users] problem with .edr file

[Anna Marabotti]

Dear gmx-users,
I launched several dynamics with gromacs 4.0.7, they finished regularly with
apparently no problems (=no error messages at the end of the runs), but when
I started analyzing the results, I found a problem in the .edr files. In
details, when I used them with g_energy, I found that only 4 of the points
that should have been saved as I stated in the .mdp file ( I set to save
energy, force, coordinates, log every 100 ps) were present in the file. The
.log files were correct and I can see energies in all the steps. I checked
both the .trr and the .edr files with gmxcheck and I found that the .trr
(and also the .xtc) files were correct, whereas the .edr files gave me the
following message error:
 
Checking energy file FAPP2-GLTPapo_md20ns1.edr
 
Opened FAPP2-GLTPapo_md20ns1.edr as single precision energy file
frame:  6 (index  0), t:120.000
Reading energy frame  2 time  300.000
Timesteps at t=200 don't match (80, 100)
Reading energy frame200 time 20100.000
Timesteps at t=20100 don't match (100, 20)
Last energy frame read 201 time 20120.000
 
Found 202 frames.
 
I used mdrun -rerun and the .trr file to obtain a new .edr file, and this
time the file was correct, with all the points present, so I think that the
run was made correctly, but the .edr was not properly saved. I don't know
why this happened: do you think it could be a problem in the Gromacs
version, or in the Gromacs installation? Any hint will be very appreciated.
Many thanks in advance and best regards
Anna

Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabo...@isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"If you think you are too small to make a difference, try sleeping with a
mosquito"
 
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