Re: [gmx-users] NAMD file (.inp) convert to GROMACS format

2012-01-27 Thread Dariush Mohammadyani 
Thanks Justin!

There is one script in User Contributions page, but it does not work.
I totally changed my way, I will use NAMD in this case...



On Fri, Jan 27, 2012 at 2:11 PM, Justin A. Lemkul  wrote:

>
>
> Dariush Mohammadyani wrote:
>
>> Is there any similar script to change it for this reason?
>>
>>
> If there is one that exists, it may have been posted to the User
> Contributions page of the Gromacs website.  If not, maybe someone will post
> one for you.
>
> I've seen this question asked before with no answer, so likely it's time
> to break out the NAMD and Gromacs manuals in concert with your favorite
> text editor and scripting language, and have at it.
>
> -Justin
>
>
>> On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Dariush Mohammadyani wrote:
>>
>>Hi all,
>>
>>I have two files (Topology and Parameter files) in NAMD format
>>(*.inp). I am going to use them in GROMACS.
>>Can you help me how can I use them?
>>
>>
>>You'll have to have a good working knowledge of all file formats
>>involved (which, for Gromacs, requires a thorough read through
>>Chapter 5 of the manual) and design a script that will parse the
>>relevant information from your existing files and write them into
>>Gromacs format.
>>
>>-Justin
>>
>>-- ==**__==
>>
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>==**__==
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
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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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-- 
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
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Re: [gmx-users] non-bonded interactions energies

2012-01-27 Thread Justin A. Lemkul 



Naomi Fox wrote:
On Fri, Jan 27, 2012 at 12:22 PM, Justin A. Lemkul > wrote:




Naomi Fox wrote:

On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 27/01/2012 12:35 PM, Naomi Fox wrote:

   I would like to print out a list of non-bonded
interactions and
   their associated LJ-potentials and coulombic potentials.

   I tried g_energy, but couldn't figure out the combination of
   parameters to get this information.


   During the simulation, you can only save the magnitude of the
   interactions between energy groups (see manual), and by
default the
   only such group is the whole system. mdrun -rerun is useful for
   re-computing quantities based on an existing simulation.

   Mark


So what you're saying is it isn't possible?  
When I rerun mdrun with the -seppot option, I see in the md.log

file that I get the VdW and Coulomb V and dVdl for node 0 (the
only node).

There is no way to print the exact contribution from each
individual interaction?


It certainly is possible, you just need to specify energygrps (in
the .mdp file) for the interactions you want to monitor, as Mark
said.  The -seppot flag is for the free energy code, IIRC, not a
magic option to dump a bunch of different interactions.

-Justin


Thanks Mark and Justin.

Two more questions:

1) How do I define an energy group for an interaction?  All I found for 
examples in the manual are "Protein" and "SOL"




You can define any group you wish with a suitable index group.

2) Can I dump all the interactions listed as [ pairs ] in the .top file? 
 I only need them for a single conformation and not for a full trajectory. 


Pair interactions are fixed quantities so they can be calculated by hand (or by 
a script, likely preferrable), otherwise you can set them as energygrps as well 
(one-atom groups).


-Justin

--


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


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Re: [gmx-users] non-bonded interactions energies

2012-01-27 Thread Naomi Fox 
On Fri, Jan 27, 2012 at 12:22 PM, Justin A. Lemkul  wrote:

>
>
> Naomi Fox wrote:
>
>  On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham 
> > mark.abra...@anu.edu.**au >> wrote:
>>
>>On 27/01/2012 12:35 PM, Naomi Fox wrote:
>>
>>I would like to print out a list of non-bonded interactions and
>>their associated LJ-potentials and coulombic potentials.
>>
>>I tried g_energy, but couldn't figure out the combination of
>>parameters to get this information.
>>
>>
>>During the simulation, you can only save the magnitude of the
>>interactions between energy groups (see manual), and by default the
>>only such group is the whole system. mdrun -rerun is useful for
>>re-computing quantities based on an existing simulation.
>>
>>Mark
>>
>>
>> So what you're saying is it isn't possible?
>> When I rerun mdrun with the -seppot option, I see in the md.log file that
>> I get the VdW and Coulomb V and dVdl for node 0 (the only node).
>>
>> There is no way to print the exact contribution from each individual
>> interaction?
>>
>>
> It certainly is possible, you just need to specify energygrps (in the .mdp
> file) for the interactions you want to monitor, as Mark said.  The -seppot
> flag is for the free energy code, IIRC, not a magic option to dump a bunch
> of different interactions.
>
> -Justin
>
>
Thanks Mark and Justin.

Two more questions:

1) How do I define an energy group for an interaction?  All I found for
examples in the manual are "Protein" and "SOL"

2) Can I dump all the interactions listed as [ pairs ] in the .top file?  I
only need them for a single conformation and not for a full trajectory.
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Re: [gmx-users] non-bonded interactions energies

2012-01-27 Thread Justin A. Lemkul 



Naomi Fox wrote:
On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham > wrote:


On 27/01/2012 12:35 PM, Naomi Fox wrote:

I would like to print out a list of non-bonded interactions and
their associated LJ-potentials and coulombic potentials.

I tried g_energy, but couldn't figure out the combination of
parameters to get this information.


During the simulation, you can only save the magnitude of the
interactions between energy groups (see manual), and by default the
only such group is the whole system. mdrun -rerun is useful for
re-computing quantities based on an existing simulation.

Mark


So what you're saying is it isn't possible?  

When I rerun mdrun with the -seppot option, I see in the md.log file 
that I get the VdW and Coulomb V and dVdl for node 0 (the only node).


There is no way to print the exact contribution from each individual 
interaction?




It certainly is possible, you just need to specify energygrps (in the .mdp file) 
for the interactions you want to monitor, as Mark said.  The -seppot flag is for 
the free energy code, IIRC, not a magic option to dump a bunch of different 
interactions.


-Justin

--


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


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Re: [gmx-users] non-bonded interactions energies

2012-01-27 Thread Naomi Fox 
On Thu, Jan 26, 2012 at 7:20 PM, Mark Abraham wrote:

> On 27/01/2012 12:35 PM, Naomi Fox wrote:
>
>> I would like to print out a list of non-bonded interactions and their
>> associated LJ-potentials and coulombic potentials.
>>
>> I tried g_energy, but couldn't figure out the combination of parameters
>> to get this information.
>>
>
> During the simulation, you can only save the magnitude of the interactions
> between energy groups (see manual), and by default the only such group is
> the whole system. mdrun -rerun is useful for re-computing quantities based
> on an existing simulation.
>
> Mark
>

So what you're saying is it isn't possible?

When I rerun mdrun with the -seppot option, I see in the md.log file that I
get the VdW and Coulomb V and dVdl for node 0 (the only node).

There is no way to print the exact contribution from each individual
interaction?
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[gmx-users] can mdrun append output files without the proper .cpt?

2012-01-27 Thread Alex Marshall 
Hi all,
I was trying to extend my simulation but I used the wrong .tpr file when I
called mdrun_mpi. I didn't catch it in time and my checkpoint files were
overwritten. Now I've used GROMPP to extend the simulation (as directed in
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations), but
when I use mdrun_mpi -append with the extended .tpr file, new output files
are generated anyway. Is there a way around this, or will I just have to
use trjcat or something once the new run has finished?
Thanks.
-- 
Alex Marshall
M.Sc. Candidate
Department of Applied Mathematics
The University of Western Ontario
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Re: [gmx-users] Gromacs on GPU

2012-01-27 Thread Justin A. Lemkul 



Matthew Lardy wrote:

Sorry to hear that, as I have had the same problem for over four
months (OpenMM 3+, Gromacs 4.5.4+, Cuda 4, etc.).  No one ever got
back to me, and I just abandoned Gromacs for Amber (who's GPU
accelerated code base compiles and works).

I would be interested to hear if the intervening time, if a plan had
been hatched to make the GPU code production quality.  If that has
indeed happened.



I don't see a corresponding issue posted to redmine.gromacs.org - has there been 
one filed?  If not, reports often get lost on the mailing list, so the only way 
to ensure action is to post a bug report.


We get junk output with 4.5.4 if the box size is set to zero, for some odd 
reason, though in principle it should be ignored with "pbc = no" in the .mdp 
file.  Using any non-zero box results in usable results.  Our OpenMM version is 
the same, but Cuda is in the 3.x series (can't remember off the top of my head, 
sorry).


-Justin

--


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


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Re: [gmx-users] NAMD file (.inp) convert to GROMACS format

2012-01-27 Thread Justin A. Lemkul 



Dariush Mohammadyani wrote:

Is there any similar script to change it for this reason?



If there is one that exists, it may have been posted to the User Contributions 
page of the Gromacs website.  If not, maybe someone will post one for you.


I've seen this question asked before with no answer, so likely it's time to 
break out the NAMD and Gromacs manuals in concert with your favorite text editor 
and scripting language, and have at it.


-Justin



On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul > wrote:




Dariush Mohammadyani wrote:

Hi all,

I have two files (Topology and Parameter files) in NAMD format
(*.inp). I am going to use them in GROMACS.
Can you help me how can I use them?


You'll have to have a good working knowledge of all file formats
involved (which, for Gromacs, requires a thorough read through
Chapter 5 of the manual) and design a script that will parse the
relevant information from your existing files and write them into
Gromacs format.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
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--


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


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Re: [gmx-users] Re: Free Energy tutorial - choosing number of solvent molecules

2012-01-27 Thread Justin A. Lemkul 



Fabian Casteblanco wrote:

Hello Justin,

I am running 2,000,000 time steps for the actual MD run (4,000 ps).
Depending on how many solvent molecules I start with, I get slightly
different results.  Do you think its ok to run several different tests
and take the average?  Or perhaps take the end results of a shorter MD
run and use those as the starting coordinates for a new run?



Either approach sounds reasonable to me.  Keep in mind magnitude - some of your 
differences were 5 kJ/mol, which may or may not be statistically relevant, 
depending on the value of DG and the resulting error estimates.


-Justin


Thanks,
Fabian




Fabian Casteblanco wrote:

Hello all,

I'm running the same process from the free energy tutorial by Justin
Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html.

How did the number of solvent particles get chosen (in the tutorial, 210
molecules were chosen)?   I seem to be getting slightly different


If memory serves, I reproduced what was in the original paper, but do check.


results (ranging from as small as 200 J/mol to about 5 kJ/mol depending
on how many molecules I choose (ranging for example from 210 ethanol
molecules to about 610 ethanol molecules for the largest energy
difference change of about 5 kJ).   I keep running tests to see if there
is some sort of minimum atom number to get steady consistent numbers but
I can't seem to find it.  When I plot for example the bar.xvg &
barint.xvg for both sets to see where the lines don't match up, its
usually one or two points that differ slightly which cause the free
energies in the end to be slightly different.I seem to be noticing
too that the more atoms I use, the free energy gets a little bit lower.

Does anybody have any experience with this?



How long are your simulations?  I have experienced the case (using a
water-octanol solvent mixture) where the initial configuration made a big
difference in the result, so longer simulations and multiple configurations for
the solvent were necessary to get reliable averages.

-Justin



--


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


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[gmx-users] diffusion coeffecient/constant

2012-01-27 Thread Ramya Parthasarathi 
Hi,

I am working with DOPC lipid molecules, I was searching the literature for the 
value of the diffusion coeffecient for DOPC. I could not find one. can some one 
tell me what the value is is it close to  (8.6 ± 0.2) × 10−12 m2/s?
 

 

Ramya Parthasarathi
ramya.sar...@aol.com

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Re: [gmx-users] Gromacs on GPU

2012-01-27 Thread Matthew Lardy 
Sorry to hear that, as I have had the same problem for over four
months (OpenMM 3+, Gromacs 4.5.4+, Cuda 4, etc.).  No one ever got
back to me, and I just abandoned Gromacs for Amber (who's GPU
accelerated code base compiles and works).

I would be interested to hear if the intervening time, if a plan had
been hatched to make the GPU code production quality.  If that has
indeed happened.

Matthew

On Fri, Jan 27, 2012 at 9:18 AM, Ben Hall  wrote:
> Hi
>
> I've been attempting to use the GPU enabled version of gromacs to run
> implicit solvent simulations, but I've run into an odd problem. I have
> downloaded and can run the benchmark simulations from the gromacs website,
> and reproduce the speeds reported there. However, when I edit the MDP
> files to write out data both the xtc and trr files contain junk data- the
> first frame is correct but every coordinate in the following frames is the
> same. These same MDP files work on the GPU disabled (default) gromacs and
> produce reasonable trajectories. As the simulations aren't crashing I
> assume that the issue relates to writing specifically; has anyone observed
> the same problem, and is there a workaround or patch?
>
> The versions of each piece of software used are
> gromacs 4.5.5
> openmm 3.1.1
> cuda 4.0
> and all compiled using intel compiler version 11.1/072
>
> Thanks in advance
>
> Ben
>
>
> --
> Dr Benjamin A Hall
> Centre for Computational Science, Department of Chemistry, UCL
> benjamin.a.h...@ucl.ac.uk
>
>
>
>
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[gmx-users] Gromacs on GPU

2012-01-27 Thread Ben Hall 
Hi

I've been attempting to use the GPU enabled version of gromacs to run
implicit solvent simulations, but I've run into an odd problem. I have
downloaded and can run the benchmark simulations from the gromacs website,
and reproduce the speeds reported there. However, when I edit the MDP
files to write out data both the xtc and trr files contain junk data- the
first frame is correct but every coordinate in the following frames is the
same. These same MDP files work on the GPU disabled (default) gromacs and
produce reasonable trajectories. As the simulations aren't crashing I
assume that the issue relates to writing specifically; has anyone observed
the same problem, and is there a workaround or patch?

The versions of each piece of software used are
gromacs 4.5.5
openmm 3.1.1
cuda 4.0
and all compiled using intel compiler version 11.1/072

Thanks in advance

Ben


-- 
Dr Benjamin A Hall
Centre for Computational Science, Department of Chemistry, UCL
benjamin.a.h...@ucl.ac.uk




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Re: [gmx-users] NAMD file (.inp) convert to GROMACS format

2012-01-27 Thread Dariush Mohammadyani 
Is there any similar script to change it for this reason?


On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul  wrote:

>
>
> Dariush Mohammadyani wrote:
>
>> Hi all,
>>
>> I have two files (Topology and Parameter files) in NAMD format (*.inp). I
>> am going to use them in GROMACS.
>> Can you help me how can I use them?
>>
>>
> You'll have to have a good working knowledge of all file formats involved
> (which, for Gromacs, requires a thorough read through Chapter 5 of the
> manual) and design a script that will parse the relevant information from
> your existing files and write them into Gromacs format.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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[gmx-users] g_kinetics and data.xvg file

2012-01-27 Thread saber naderi 
Dear gmx-users,

I have two questions regarding data.xvg file that is used as an input for
g_kinetics. According to manual, this file contains data "that can be
interpreted as an indicator for folding". My questions are:
- Does it contain columns of data for different temperatures that are
indicated in the temp.xvg file?
- Is this data obtained from the trajectories that are continues with
respect to ensemble or from the ones that are continues with respect to
simulation time?

Best regards,
Sab
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[gmx-users] Re: Free Energy tutorial - choosing number of solvent molecules

2012-01-27 Thread Fabian Casteblanco 
Hello Justin,

I am running 2,000,000 time steps for the actual MD run (4,000 ps).
Depending on how many solvent molecules I start with, I get slightly
different results.  Do you think its ok to run several different tests
and take the average?  Or perhaps take the end results of a shorter MD
run and use those as the starting coordinates for a new run?

Thanks,
Fabian




Fabian Casteblanco wrote:
> Hello all,
>
> I'm running the same process from the free energy tutorial by Justin
> Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html.
>
> How did the number of solvent particles get chosen (in the tutorial, 210
> molecules were chosen)?   I seem to be getting slightly different

If memory serves, I reproduced what was in the original paper, but do check.

> results (ranging from as small as 200 J/mol to about 5 kJ/mol depending
> on how many molecules I choose (ranging for example from 210 ethanol
> molecules to about 610 ethanol molecules for the largest energy
> difference change of about 5 kJ).   I keep running tests to see if there
> is some sort of minimum atom number to get steady consistent numbers but
> I can't seem to find it.  When I plot for example the bar.xvg &
> barint.xvg for both sets to see where the lines don't match up, its
> usually one or two points that differ slightly which cause the free
> energies in the end to be slightly different.I seem to be noticing
> too that the more atoms I use, the free energy gets a little bit lower.
>
> Does anybody have any experience with this?
>

How long are your simulations?  I have experienced the case (using a
water-octanol solvent mixture) where the initial configuration made a big
difference in the result, so longer simulations and multiple configurations for
the solvent were necessary to get reliable averages.

-Justin

-- 


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





On Thu, Jan 26, 2012 at 11:21 AM, Fabian Casteblanco
 wrote:
>
> Hello all,
>
> I'm running the same process from the free energy tutorial by Justin 
> Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html.
>
> How did the number of solvent particles get chosen (in the tutorial, 210 
> molecules were chosen)?   I seem to be getting slightly different results 
> (ranging from as small as 200 J/mol to about 5 kJ/mol depending on how many 
> molecules I choose (ranging for example from 210 ethanol molecules to about 
> 610 ethanol molecules for the largest energy difference change of about 5 
> kJ).   I keep running tests to see if there is some sort of minimum atom 
> number to get steady consistent numbers but I can't seem to find it.  When I 
> plot for example the bar.xvg & barint.xvg for both sets to see where the 
> lines don't match up, its usually one or two points that differ slightly 
> which cause the free energies in the end to be slightly different.    I seem 
> to be noticing too that the more atoms I use, the free energy gets a little 
> bit lower.
>
> Does anybody have any experience with this?
>
> Thanks.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> C: +908 917 0723
> E:  fabian.castebla...@gmail.com
>



--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] NAMD file (.inp) convert to GROMACS format

2012-01-27 Thread Justin A. Lemkul 



Dariush Mohammadyani wrote:

Hi all,

I have two files (Topology and Parameter files) in NAMD format (*.inp). 
I am going to use them in GROMACS.

Can you help me how can I use them?



You'll have to have a good working knowledge of all file formats involved 
(which, for Gromacs, requires a thorough read through Chapter 5 of the manual) 
and design a script that will parse the relevant information from your existing 
files and write them into Gromacs format.


-Justin

--


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


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[gmx-users] high forces

2012-01-27 Thread francesco oteri 
Dear gromacs users,
I  am attempting to simulate a protein with an active site containing to
metals (Ni and Fe). I am trying to mantain the active site structure
constraining bonds, angles and dihedrals.
When I simulate the active site alone in water, it remains stable. When I
insert the active site in the protein's scaffold, unfortunately,
the simulation crashes because of large vibration in bond lenght and angle
amplitude in the active site. I am not able to detect big clashes or any
structural distortion.

I tried to play with force constants, temperature, time-step, constrains,
etc.etc. but I am not able to mantain the simulation stability.

I am wondering whether exists a tool to dissect the energetic contributions
( including bonded parameters ) permitting me to identify the problem
giving rise the crash.

Francesco
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[gmx-users] NAMD file (.inp) convert to GROMACS format

2012-01-27 Thread Dariush Mohammadyani 
Hi all,

I have two files (Topology and Parameter files) in NAMD format (*.inp). I
am going to use them in GROMACS.
Can you help me how can I use them?


Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
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Re: [gmx-users] MMPBSA

2012-01-27 Thread Mark Abraham 

On 28/01/2012 12:54 AM, shahid nayeem wrote:

Dear All
 I have done MMPBSA calculation on some complexes. It calculates 
energy in terms of polar contribution to solvation as PBSUR and 
nonpolar contribution to solvation as PBCAL and sum of these two terms 
as PBSOL. It appears to me that PBSOL is the desolvaion component of 
binding free energy but I am not sure. If  it is desolvation then why 
polar and nonpolar contribution to solvation is written. Please help me.

Shahid Nayeem



This question is off-topic for this mailing list. Please consider an 
alternative.


Mark
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[gmx-users] reverse transformation

2012-01-27 Thread francesca vitalini 
Hi!
I posted a message before regarding the reverse transformation with g_fg2cg
command. Now I have managed to re-numerate correctly the residues so that
it doesn't complain about it but I have come across a different problem.
when I run the command it doesn't recognize the ions NA+. So I was
wondering if the ions are mapped in the fg_w.itp files and how or if there
is an appropriate .itp file for mapping the ions from cg to fg.
Thanks
Francesca
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Re: [gmx-users] A query

2012-01-27 Thread Mark Abraham 

On 27/01/2012 9:50 PM, Anik Sen wrote:

Hello,
  Am anik. Am using gromacs 4.5.5
I could not find the proper reason of the foillowig failure of my job. 
please help.


The following is a part of the dna pdb file, which I am using:

ATOM  1  OH  DG5 X   1  13.663  36.760  21.465  0.00  0.00
ATOM  2  CT  DG5 X   1  14.791  36.040  21.150  0.00  0.00
ATOM  3  CT  DG5 X   1  14.771  34.703  21.873  0.00  0.00
ATOM  4  OS  DG5 X   1  16.017  34.553  22.577  0.00  0.00
ATOM  5  CT  DG5 X   1  13.724  34.528  22.970  0.00  0.00
ATOM  6  OS  DG5 X   1  13.540  33.118  23.234  0.00  0.00


The third column here is the atom name, the fourth is the residue name.





I am using amber 03 forcefield (amber03.ff) whose atom type is as follows:

H0 1.00800  ; H aliph. bond. to C with 1 electrwd. 
group (03GLY)

Br79.9; bromine
C 12.01000; sp2 C carbonyl group
CA12.01000; sp2 C pure aromatic (benzene)
CB12.01000; sp2 aromatic C, 5&6 membered ring junction
CC12.01000; sp2 aromatic C, 5 memb. ring HIS
CK12.01000; sp2 C 5 memb.ring in purines
CM12.01000; sp2 C  pyrimidines in pos. 5 & 6
..


The dna-rtp file in the amber 03 is as follows:

[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove impropers over the same bond as a proper if it is 1
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
 1   1  9  41 3  1 0


; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's

[ DA5 ]
 [ atoms ]
   H5THO0.44220 1
   O5'OH   -0.63180 2
   C5'CT   -0.00690 3
  H5'1H10.07540 4

[ DG5 ]
 [ atoms ]
   H5THO0.44220 1
   O5'OH   -0.63180 2
   C5'CT   -0.00690 3
  H5'1H10.07540 4
  H5'2H10.07540 5
   C4'CT0.16290 6
   H4'H10.11760 7
   O4'OS   -0.36910 8
   C1'CT0.03580 9
...


The first column here is the atom name, the second column is the atom 
type. pdb2gmx has to be able to match atom names in the .pdb file with 
those here, for the given residue. In your case, it can't. You will need 
to rename the atoms in the .pdb file, somehow. When you do, make sure 
you preserve the column formatting of the .pdb file.


Mark



But then also when I am running the file with the command:

pdb2gmx -f dna5.pdb -o dnA5.pdb -p topol.top
 with TIP3P water model
I am getting the following error:

Identified residue DG51 as a starting terminus.
Warning: Residue Na2 in chain has different type (Ion) from starting 
residue DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting 
residue DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting 
residue DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting 
residue DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting 
residue DG51 (DNA).
More than 5 unidentified residues at end of chain - disabling further 
warnings.

Identified residue DG51 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn


---
Program pdb2gmx, VERSION 4.5.5
Source code file: pdb2gmx.c, line: 655

Fatal error:
Atom OH in residue DG5 1 was not found in rtp entry DG5 with 31 atoms
while sorting atoms.


Thanks in advance


Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
www.csmcri.org





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[gmx-users] rules of thumb to select a cutoff for clustering

2012-01-27 Thread Thomas Evangelidis 
I know that this topic has been mentioned again in the mailing list, yet no
explicit answer has been given. So my questions are:

1. How can I utilize the output files of g_cluster (rms-distribution.xvg,
cluster-sizes.xvg, cluster-id-over-time.xvg, cluster-transitions* ) to
decide which is the best cutoff to use with the gromos algorithm for my
analysis?

2. What do these warning messages mean and how can I use them for the
cutoff decision?

WARNING: rmsd cutoff 1.2 is outside range of rmsd values 0.0283 to 0.559
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0283


I would greatly appreciate any advice!

Thomas





-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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[gmx-users] A query

2012-01-27 Thread Anik Sen 
Hello,
  Am anik. Am using gromacs 4.5.5
I could not find the proper reason of the foillowig failure of my job. please 
help.

The following is a part of the dna pdb file, which I am using:

ATOM  1  OH  DG5 X   1  13.663  36.760  21.465  0.00  0.00
ATOM  2  CT  DG5 X   1  14.791  36.040  21.150  0.00  0.00
ATOM  3  CT  DG5 X   1  14.771  34.703  21.873  0.00  0.00
ATOM  4  OS  DG5 X   1  16.017  34.553  22.577  0.00  0.00
ATOM  5  CT  DG5 X   1  13.724  34.528  22.970  0.00  0.00
ATOM  6  OS  DG5 X   1  13.540  33.118  23.234  0.00  0.00


I am using amber 03 forcefield (amber03.ff) whose atom type is as follows:

H0 1.00800  ; H aliph. bond. to C with 1 electrwd. group 
(03GLY)
Br79.9; bromine
C 12.01000; sp2 C carbonyl group
CA12.01000; sp2 C pure aromatic (benzene)
CB12.01000; sp2 aromatic C, 5&6 membered ring junction
CC12.01000; sp2 aromatic C, 5 memb. ring HIS
CK12.01000; sp2 C 5 memb.ring in purines
CM12.01000; sp2 C  pyrimidines in pos. 5 & 6
..


The dna-rtp file in the amber 03 is as follows:

[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove impropers over the same bond as a proper if it is 1
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
 1   1  9  41 3  1 0


; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's

[ DA5 ]
 [ atoms ]
   H5THO0.44220 1
   O5'OH   -0.63180 2
   C5'CT   -0.00690 3
  H5'1H10.07540 4

[ DG5 ]
 [ atoms ]
   H5THO0.44220 1
   O5'OH   -0.63180 2
   C5'CT   -0.00690 3
  H5'1H10.07540 4
  H5'2H10.07540 5
   C4'CT0.16290 6
   H4'H10.11760 7
   O4'OS   -0.36910 8
   C1'CT0.03580 9
...

But then also when I am running the file with the command:

pdb2gmx -f dna5.pdb -o dnA5.pdb -p topol.top
 with TIP3P water model
I am getting the following error:

Identified residue DG51 as a starting terminus.
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
More than 5 unidentified residues at end of chain - disabling further warnings.
Identified residue DG51 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn

---
Program pdb2gmx, VERSION 4.5.5
Source code file: pdb2gmx.c, line: 655

Fatal error:
Atom OH in residue DG5 1 was not found in rtp entry DG5 with 31 atoms
while sorting atoms.


Thanks in advance


Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[www.csmcri.org]

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[gmx-users] (no subject)

2012-01-27 Thread Anik Sen 
The following is a part of the dna pdb file, which I am using:

ATOM  1  OH  DG5 X   1  13.663  36.760  21.465  0.00  0.00
ATOM  2  CT  DG5 X   1  14.791  36.040  21.150  0.00  0.00
ATOM  3  CT  DG5 X   1  14.771  34.703  21.873  0.00  0.00
ATOM  4  OS  DG5 X   1  16.017  34.553  22.577  0.00  0.00
ATOM  5  CT  DG5 X   1  13.724  34.528  22.970  0.00  0.00
ATOM  6  OS  DG5 X   1  13.540  33.118  23.234  0.00  0.00


I am using amber 03 forcefield (amber03.ff) whose atom type is as follows:

H0 1.00800  ; H aliph. bond. to C with 1 electrwd. group 
(03GLY)
Br79.9; bromine
C 12.01000; sp2 C carbonyl group
CA12.01000; sp2 C pure aromatic (benzene)
CB12.01000; sp2 aromatic C, 5&6 membered ring junction
CC12.01000; sp2 aromatic C, 5 memb. ring HIS
CK12.01000; sp2 C 5 memb.ring in purines
CM12.01000; sp2 C  pyrimidines in pos. 5 & 6
..


The dna-rtp file in the amber 03 is as follows:

[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove impropers over the same bond as a proper if it is 1
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
 1   1  9  41 3  1 0


; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's

[ DA5 ]
 [ atoms ]
   H5THO0.44220 1
   O5'OH   -0.63180 2
   C5'CT   -0.00690 3
  H5'1H10.07540 4

[ DG5 ]
 [ atoms ]
   H5THO0.44220 1
   O5'OH   -0.63180 2
   C5'CT   -0.00690 3
  H5'1H10.07540 4
  H5'2H10.07540 5
   C4'CT0.16290 6
   H4'H10.11760 7
   O4'OS   -0.36910 8
   C1'CT0.03580 9
...

But then also when I am running the file with the command:

pdb2gmx -f dna5.pdb -o dnA5.pdb -p topol.top
 with TIP3P water model
I am getting the following error:

Identified residue DG51 as a starting terminus.
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting residue 
DG51 (DNA).
More than 5 unidentified residues at end of chain - disabling further warnings.
Identified residue DG51 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file 
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn

---
Program pdb2gmx, VERSION 4.5.5
Source code file: pdb2gmx.c, line: 655

Fatal error:
Atom OH in residue DG5 1 was not found in rtp entry DG5 with 31 atoms
while sorting atoms.



Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[www.csmcri.org]

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Re: [gmx-users] Wildcards and dihedral type 9

2012-01-27 Thread Mark Abraham 

On 27/01/2012 8:59 PM, Mark Abraham wrote:

On 27/01/2012 6:22 PM, Antila Hanne wrote:

Dear experts,

I'm a bit confused about the use wildcards in the dihedral definitions
of .itp force field files. I'm under the impression that explicit
definition of a dihedral (e.g. OS-CT-CT-OS) is always used if
available and it overwrites any wildcards (for example X-CT-CT-X) that
might match that particular dihedral. However:

1. Does the explicit definition replace wildcard if they have
different periodicity. That is, are the expressions matched based on
atom types alone or atom types and periodicity?


Don't know, but if you make a simple test case, you can use gmxdump to 
see what grompp decided to do. Note that the output of gmxdump starts 
numbering from zero, not one.


Easier still is to make a local copy of the forcefield folder, run 
grompp using the normal version. Then change one thing that will test 
the effect of the above. Re-run grompp and use gmxcheck to compare the 
"before and after" .tpr files.


Mark





2. Does the use of dihedral type 9, which enables summation of several
(type 1) dihedrals, have an effect on this?


I doubt it.

Mark



  Thanks for the help!

  Hanne Antila
  Phd student
  Aalto University
  Finland--
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Re: [gmx-users] Wildcards and dihedral type 9

2012-01-27 Thread Mark Abraham 

On 27/01/2012 6:22 PM, Antila Hanne wrote:

Dear experts,

I'm a bit confused about the use wildcards in the dihedral definitions
of .itp force field files. I'm under the impression that explicit
definition of a dihedral (e.g. OS-CT-CT-OS) is always used if
available and it overwrites any wildcards (for example X-CT-CT-X) that
might match that particular dihedral. However:

1. Does the explicit definition replace wildcard if they have
different periodicity. That is, are the expressions matched based on
atom types alone or atom types and periodicity?


Don't know, but if you make a simple test case, you can use gmxdump to 
see what grompp decided to do. Note that the output of gmxdump starts 
numbering from zero, not one.




2. Does the use of dihedral type 9, which enables summation of several
(type 1) dihedrals, have an effect on this?


I doubt it.

Mark



  Thanks for the help!

  Hanne Antila
  Phd student
  Aalto University
  Finland--
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.
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