[gmx-users] Re: gmx-users Digest, Vol 86, Issue 84

[Ravi Kumar Venkatraman]

Dear Sir/Madam,
 Please help me to find that why we need to run NVT
and then NPT in equilibriation run and not the vice-versa.

Thank you in advance

Ravi Kumar V

IPC dept.,
IISC,
INDIA.
-- 
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

Re: [gmx-users] Re: gmx-users Digest, Vol 86, Issue 84

[Mark Abraham]

On 14/06/2011 5:10 PM, Ravi Kumar Venkatraman wrote:



Dear Sir/Madam,
 Please help me to find that why we need to 
run NVT and then NPT in equilibriation run and not the vice-versa.


See 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation


Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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

Re: [gmx-users] data points missing

[Mark Abraham]

On 14/06/2011 4:24 PM, Kavyashree M wrote:

Dear users,

   In one of the simulations I have run, I have transfered
it from one system to another so some data points were missing
what I should do now. how to find which data points are missing?


I don't agree with your guess that transferring to new hardware is the 
reason for your missing data. How are you determining that data is 
missing if you aren't finding out what data is missing? Please try to 
provide complete information if you want to attract people to donate 
their time to help you. They have better things to do than ask 
diagnostic questions :-)


Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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

[gmx-users] Re: data points missing

[Kavyashree M]

Dear users,

 gmxcheck on the .xtc file shows that simulation has run for 100ns
but while calculating energy terms using ener.edr file, it gives "nan" error
-

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature 300  9e-05   -nan -0.000501989  (K)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure0.99914  0.027   -nan  0.0174391  (bar)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Volume  517.755 0.0094   -nan   0.010871  (nm^3)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Density 1012.53  0.018   -nan -0.0216399
(kg/m^3)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Kinetic En.  129266  0.039   -nan  -0.216264
(kJ/mol)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential   -710705 62   -nan   -394.425
(kJ/mol)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Total Energy-581438 62   -nan   -394.641
(kJ/mol)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Coul-SR:Protein-Protein-26868.2 97   -nan   -674.338
(kJ/mol)
Coul-14:Protein-Protein 28921.79.1   -nan47.6164
(kJ/mol)
Coul-SR:Protein-non-Protein   -27393.6160   -nan1050.26
(kJ/mol)
Coul-14:Protein-non-Protein  0  0   -nan  0
(kJ/mol)
Coul-SR:non-Protein-non-Protein-742644 92   -nan   -622.378
(kJ/mol)
Coul-14:non-Protein-non-Protein  0  0   -nan  0
(kJ/mol)

an number of data points is only  1978700 compared to actual data points
of 501. where could be the error? and is it possible to get the missing
data
points?

Thanks
With regards
M. Kavyashree

On Tue, Jun 14, 2011 at 11:54 AM, Kavyashree M  wrote:

> Dear users,
>
>In one of the simulations I have run, I have transfered
> it from one system to another so some data points were missing
> what I should do now. how to find which data points are missing?
>
> Thank you
> With regards
> M. Kavyashree
>
-- 
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

Re: [gmx-users] Re: data points missing

[Mark Abraham]

On 14/06/2011 6:09 PM, Kavyashree M wrote:

Dear users,

 gmxcheck on the .xtc file shows that simulation has run for 100ns
but while calculating energy terms using ener.edr file, it gives "nan" 
error -


Sounds like you have managed to calculate only on a subset of your data. 
I'm guessing that g_energy reports the RMSD as calculated from a 
quantity that is updated as the simulation progresses, and when the 
input file you're using doesn't correspond to the whole time interval, 
that quantity computes wrongly.




Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature 300  9e-05   -nan 
-0.000501989  (K)


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure0.99914  0.027   -nan  0.0174391  
(bar)


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Volume  517.755 0.0094   -nan   0.010871  
(nm^3)


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Density 1012.53  0.018   -nan -0.0216399  
(kg/m^3)


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Kinetic En.  129266  0.039   -nan  -0.216264  
(kJ/mol)


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential   -710705 62   -nan   -394.425  
(kJ/mol)


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Total Energy-581438 62   -nan   -394.641  
(kJ/mol)


Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Coul-SR:Protein-Protein-26868.2 97   -nan   -674.338  
(kJ/mol)
Coul-14:Protein-Protein 28921.79.1   -nan47.6164  
(kJ/mol)
Coul-SR:Protein-non-Protein   -27393.6160   -nan
1050.26  (kJ/mol)
Coul-14:Protein-non-Protein  0  0   -nan  
0  (kJ/mol)
Coul-SR:non-Protein-non-Protein-742644 92   -nan   
-622.378  (kJ/mol)
Coul-14:non-Protein-non-Protein  0  0   
-nan  0  (kJ/mol)


an number of data points is only  1978700 compared to actual data points
of 501. where could be the error? and is it possible to get the 
missing data

points?


You can't get the missing data from the file from which it is missing. 
Whether you have any other files is something only you know.


Also, 500 data points from 100ns is collecting data far too often 
for most purposes. Quantities from adjacent time steps are strongly 
correlated, and gathering extra data points that are highly correlated 
with existing data points gains correspondingly little.


Mark


Thanks
With regards
M. Kavyashree

On Tue, Jun 14, 2011 at 11:54 AM, Kavyashree M > wrote:


Dear users,

   In one of the simulations I have run, I have transfered
it from one system to another so some data points were missing
what I should do now. how to find which data points are missing?

Thank you
With regards
M. Kavyashree




-- 
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

[gmx-users] Re: Dissociation of Ligand-reg

[ITHAYARAJA]

Sir,

The simulation system consists of enzyme, two substrate and one native
ligand (protein, glutathione and NADPH + FAD) actually I am interested in
manifesting substrate (GSH of GSSG and NADP+ of NADPH) dissociation from the
protein after reduction reaction. I here below mentioned an article
reference for your notice, likewise can we do simulation work?


Dong Long, Yuguang Mu, Daiwen Yang "Molecular Dynamics Simulation of Ligand
Dissociation
from Liver Fatty Acid Binding Protein" Plos, 2009.




On 13 June 2011 10:09, ITHAYARAJA  wrote:

>
> Dear Sir,
>
> Greeting!
>
> I convey my thanks to your kind reply for rising whatever doubts and
> troubles in gromacs.
>
> I able to do my simulation with desire ligand following your instruction.
> Now I am interested to simulate the dissociation of bound ligand
> particularly one molecule among three. Sir, I need your help to do this
> dynamics study. I also went through some article which refers to SMD, TMD,
> IMD, REMD and AFM pulling able to do the job. So, Kindly instruct me which
> one can support gromacs for ligand dissociation simulation and What are the
> parameter set ?
>
> Thanks in advance
>
>
> Kind regards with,
>
> --
> **
> Ithayaraja M,
> Research Scholar,
> Department of Bionformatics,
> Bharathiar University,
> Coimbatore 641 046,
> Tamil Nadu
> India
>



-- 
**
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India
-- 
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

Re: [gmx-users] Regarding H-bond autocorrelation

[bipin singh]

I am using the Gromacs 4.5.3is  that feature is present in
this version..

On Mon, Jun 13, 2011 at 21:39, Erik Marklund  wrote:
> Hi,
>
> The problem is that g_hbond subtracts a "background level" to compensate for 
> the finite size of the system. I thought that feature had been taken away, 
> however. Are you using old code?
>
> Erik
>
> 12 jun 2011 kl. 19.33 skrev bipin singh:
>
>> Hello,
>>
>> I am calculating the H-bond autocorrelation using g_hbond for my
>> system, but after plotting
>> I have observed that the value for c(t) is reaching to negative, as
>> far as I know it can not be
>> negative as the probability can not be negative...please suggest
>> where is the problem..
>>
>> --
>> ---
>> Thanks and Regards,
>> Bipin Singh
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/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
>
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/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
>



-- 
---
Regards,
Bipin Singh
--
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

[gmx-users] g_sas index files/hydrogen bonds

[Marzinek, Jan]

Dear Gromacs Users,

I am calculating the hydrophobic interface area using g_sas between ligands 
(their hydrophobic solvent accessible surface area (SASA) >95%) and hydrophobic 
residues of coiled coil fragment of protein (two helical strands) as follows:

Protein SASA + ligand SASA - Protein&Ligand SASA = Interface Area between 
ligands protein

I obtained the hydrophobic interface area increasing during the simulation time 
-> so everything seems to be ok, because from my simulation 10 ligands occupy 
hydrophobic residues (the helical terminal strands open allowing ligands to 
come inside the protein).
However, 10 ligands aggregates during the simulation covering their hydrophobic 
surface which obviously has the influence on the final interface between 
protein and ligands.
Do you know how to calculate the interface area between all 10 ligands during 
the simulation time in order to subtract from final result? How should I define 
index files?

The second question: I also calculated the hydrogen bonds between ligands and 
the protein. What is interesting: app. 70% of hydrogen bonds between 
hydrophobic ligands are formed with HYDROPHILIC residues of protein. Any clue 
what is happening as final conformation involve ligands between hydrophobic 
surfaces of the protein?

All the best,

Jan
-- 
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

Re: [gmx-users] MD - analysis

[Justin A. Lemkul]

Kavyashree M wrote:

Dear Sir,

   g_mindist analysis showed the violation of minimum image convention, it
was violated over a short period of time and then it came back to normal.
I attach the plot herewith. Should this data be discarded or any useful 
information

can be obtained.



You've got a considerable number of data points wherein the periodic image 
distance is less than the longest cutoff, so I don't think you can simply shrug 
this off.  The data were influenced by spurious interactions.  Watch the 
trajectory, see what's happening during this period, and accommodate for such 
events in a new simulation based on what you learn.


-Justin


Thank you
With Regards
M. Kavyashree








--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

Re: [gmx-users] Re: Dissociation of Ligand-reg

[Justin A. Lemkul]

ITHAYARAJA wrote:

Sir,

The simulation system consists of enzyme, two substrate and one native 
ligand (protein, glutathione and NADPH + FAD) actually I am interested 
in manifesting substrate (GSH of GSSG and NADP+ of NADPH) dissociation 
from the protein after reduction reaction. I here below mentioned an 
article reference for your notice, likewise can we do simulation work?




Presumably.  Whether or not the same methods are applicable are for you to 
decide.

-Justin



Dong Long, Yuguang Mu, Daiwen Yang "Molecular Dynamics Simulation of 
Ligand Dissociation

from Liver Fatty Acid Binding Protein" Plos, 2009.




On 13 June 2011 10:09, ITHAYARAJA > wrote:



Dear Sir,

Greeting!

I convey my thanks to your kind reply for rising whatever doubts and
troubles in gromacs.

I able to do my simulation with desire ligand following your
instruction. Now I am interested to simulate the dissociation of
bound ligand particularly one molecule among three. Sir, I need your
help to do this dynamics study. I also went through some article
which refers to SMD, TMD, IMD, REMD and AFM pulling able to do the
job. So, Kindly instruct me which one can support gromacs for ligand
dissociation simulation and What are the parameter set ?

Thanks in advance


Kind regards with,

-- 
**

Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India




--
**
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

Re: [gmx-users] g_sas index files/hydrogen bonds

[Mark Abraham]

On 14/06/11, "Marzinek, Jan"   wrote:
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dear Gromacs Users,
> 
> 
>  
> 
> 
> I am calculating the hydrophobic interface area using g_sas between ligands 
> (their hydrophobic solvent accessible surface area (SASA) >95%) and 
> hydrophobic residues of coiled coil fragment of protein (two helical strands) 
> as follows:
> 
> 
>  
> 
> 
> Protein SASA + ligand SASA – Protein&Ligand SASA = Interface Area between 
> ligands protein
> 
> 
> 
>  
> 
> 
> I obtained the hydrophobic interface area increasing during the simulation 
> time -> so everything seems to be ok, because from my simulation 10 ligands 
> occupy hydrophobic residues (the helical terminal strands open allowing 
> ligands to come
>  inside the protein).
> 
> 
> However, 10 ligands aggregates during the simulation covering their 
> hydrophobic surface which obviously has the influence on the final interface 
> between protein and ligands.
> 
> 
> 
> Do you know how to calculate the interface area between all 10 ligands during 
> the simulation time in order to subtract from final result? 
> 
> 
> 
> 
> 

Isn't this the same as the above procedure, but pairwise between ligands?


> 
> 
> 
> 
> How should I define index files?
> 
> 
>  
> 
> 
> The second question: I also calculated the hydrogen bonds between ligands and 
> the protein. What is interesting: app. 70% of hydrogen bonds between 
> hydrophobic ligands are formed with HYDROPHILIC residues of protein. Any clue 
> what is happening
>  as final conformation involve ligands between hydrophobic surfaces of the 
> protein?
> 
> 
> 
> 
> 
> 

Hydrophilic residues have more hydrogen-bonding groups than hydrophobic groups? 
Some indexing mis-match? The residue type labels are too simplistic?

Mark









-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/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

Re: [gmx-users] Regarding H-bond autocorrelation

[Erik Marklund]

Could be. But, if memory serves me right, there's another dataset in the 
output, which shows the acf without the "background subtraction".

Erik

14 jun 2011 kl. 12.10 skrev bipin singh:

> I am using the Gromacs 4.5.3is  that feature is present in
> this version..
> 
> On Mon, Jun 13, 2011 at 21:39, Erik Marklund  wrote:
>> Hi,
>> 
>> The problem is that g_hbond subtracts a "background level" to compensate for 
>> the finite size of the system. I thought that feature had been taken away, 
>> however. Are you using old code?
>> 
>> Erik
>> 
>> 12 jun 2011 kl. 19.33 skrev bipin singh:
>> 
>>> Hello,
>>> 
>>> I am calculating the H-bond autocorrelation using g_hbond for my
>>> system, but after plotting
>>> I have observed that the value for c(t) is reaching to negative, as
>>> far as I know it can not be
>>> negative as the probability can not be negative...please suggest
>>> where is the problem..
>>> 
>>> --
>>> ---
>>> Thanks and Regards,
>>> Bipin Singh
>>> --
>>> 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
>> 
>> ---
>> Erik Marklund, PhD student
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,75124 Uppsala, Sweden
>> phone:+46 18 471 4537fax: +46 18 511 755
>> er...@xray.bmc.uu.se
>> http://www2.icm.uu.se/molbio/elflab/index.html
>> 
>> --
>> 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
>> 
> 
> 
> 
> -- 
> ---
> Regards,
> Bipin Singh
> --
> 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

---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

--
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

[gmx-users] rdf

[Nilesh Dhumal]

Hello,

I have a system with 128 emi (cations) and 128 Cl (anions).

I want to study is there any bifurcated interaction between hydrogen of
cation and CL atoms or CL atom interacting with 2 different hydrogen of
cation.

For this I considered all CL atoms are distinguishable.

I am thinking to run rdf between each hydrogen and each cl atom (RDF 128
times).

In my index file I made 3 groups for 3 different hydrogen and 128 groups
for 128 cl atoms.

I have to run 128 * 3 = 384 times rdf

Is this the correct way? Is there any other easier way to do this?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh








-- 
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

Re: [gmx-users] rdf

[Mark Abraham]

On 14/06/2011 10:11 PM, Nilesh Dhumal wrote:

Hello,

I have a system with 128 emi (cations) and 128 Cl (anions).

I want to study is there any bifurcated interaction between hydrogen of
cation and CL atoms or CL atom interacting with 2 different hydrogen of
cation.

For this I considered all CL atoms are distinguishable.

I am thinking to run rdf between each hydrogen and each cl atom (RDF 128
times).


There are various tools to measure distances between index groups. Check 
out chapter 8.


Mark


In my index file I made 3 groups for 3 different hydrogen and 128 groups
for 128 cl atoms.

I have to run 128 * 3 = 384 times rdf

Is this the correct way? Is there any other easier way to do this?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh










--
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

[gmx-users] Problem with 512 membrane

[Du Jiangfeng (BIOCH)]

Dear Gro users,
We created an all-atom system with 512 DPPCs by the method which was suggested 
by Justin (genconf -f 128.gro -o 512.gro -nbox 2 2 1) and a CG system with 512 
DSPCs by using Martini self assembly tutorial. We do get nice bilayers, however 
after minimization, the systems break apart. 
Also, if we add ions into the system, it also breaks apart. 
Our question is: What  causes the membrane to break apart during the 
minimization process? does it mean that 512 lipids' system is not stable or is 
it a minimization method problem?
By the way, the minimization of a 128 lipids system has no problem.

Albert and Jiang.
--
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

Re: [gmx-users] Problem with 512 membrane

[Justin A. Lemkul]

Du Jiangfeng (BIOCH) wrote:

Dear Gro users, We created an all-atom system with 512 DPPCs by the method
which was suggested by Justin (genconf -f 128.gro -o 512.gro -nbox 2 2 1) and
a CG system with 512 DSPCs by using Martini self assembly tutorial. We do get
nice bilayers, however after minimization, the systems break apart. Also, if


Please define what "break apart" means - does the system explode, or do the 
molecules simply split across PBC?



we add ions into the system, it also breaks apart. Our question is: What


Simply by adding ions?  Or by doing EM afterwards?


causes the membrane to break apart during the minimization process? does it
mean that 512 lipids' system is not stable or is it a minimization method
problem? By the way, the minimization of a 128 lipids system has no problem.



Then maybe there is some clash in the system, although I'd be surprised if this 
was the case.  Assembling what essentially amount to periodic replicates via 
genconf should be a robust procedure.  If your EM is indeed blowing up, then the 
log file (or screen output) should indicate where the high forces are.  If 
that's the case, check the structure in your favorite visualization program and 
see what's wrong in that location.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

[gmx-users] mdrun -nc

[Hsin-Lin Chiang]

Hi,

I tried gromacs 4.5.4 in these days and last version I used is 4.0.5.
I found when I add --enable-threads in installation.
I can use mdrun -nc 12 to run 12 CPUs together within one machine.
It also amazing me when I type "top" to check the job, only one process 
in computer and the CPU utility is 1200%!!
But I tried to execute it on two machines, then the second machines 
didn't work.


I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi.
That make me confused.
Am I right to use mdrun -nc to run parallel job in this way?
Does the result is the same as which is employed by mdrun_mpi?
(Exactly I never use mdrun_mpi more than one machine since the ethernet 
between machines is very slow here.)


If mdrun -nc is available.
Do we have another commend support CPUs more than one in the same machine.

Sincerely yours,
Hsin-Lin
--
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

Re: [gmx-users] mdrun -nc

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:

Hi,

I tried gromacs 4.5.4 in these days and last version I used is 4.0.5.
I found when I add --enable-threads in installation.
I can use mdrun -nc 12 to run 12 CPUs together within one machine.


I assume you mean -nt?

It also amazing me when I type "top" to check the job, only one process 
in computer and the CPU utility is 1200%!!


Sounds about right.  I see the same on my dual-core workstation.  One process, 2 
threads, and just less than 200% CPU usage.


But I tried to execute it on two machines, then the second machines 
didn't work.




You can't execute threads over multiple machines.  For that you need MPI, not 
threading (they are mutually exclusive).  You haven't provided much detail on 
what you actually did in this case and "didn't work" doesn't exactly provide any 
relevant diagnostic information.



I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi.
That make me confused.
Am I right to use mdrun -nc to run parallel job in this way?


For a single, multi-core workstation, mdrun -nt is correct.


Does the result is the same as which is employed by mdrun_mpi?


A variety of factors influence whether or not the results are the same.

http://www.gromacs.org/Documentation/Terminology/Reproducibility

(Exactly I never use mdrun_mpi more than one machine since the ethernet 
between machines is very slow here.)


If mdrun -nc is available.
Do we have another commend support CPUs more than one in the same machine.



That's what threading is doing, assuming you're invoking the command correctly. 
 As stated above, the option is -nt, not -nc.  mdrun doesn't check for whether 
or not command line arguments are actually valid, so if you're using -nc you're 
not actually doing threading, but the 1200% usage suggests you probably are.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

[shivangi nangia]

Thanks Justin, vdwradii.dat suggestion worked :)



On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul  wrote:

>
>
> shivangi nangia wrote:
>
>> Hello dear gmx-users,
>>
>> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as
>> the solvent ( with a positively charged protein and few DHB anions) in a
>> box.
>>
>> I have created the .itp and .gro file of DHB using PRODRG.
>>
>>
> Unrelated advice - the topology is probably useless unless you've corrected
> the charges.  See the paper linked from:
>
> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>
>
>  I am able to create the system, but when I try to energy minimize the
>> system I get the message:
>>
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.0e+01
>>   Number of steps=5
>> Step=   14, Dmax= 1.2e-06 nm, Epot=  9.04353e+19 Fmax= inf, atom=
>> 2781
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 10
>>
>> Double precision normally gives you higher accuracy.
>>
>> writing lowest energy coordinates.
>>
>> Back Off! I just backed up em.gro to ./#em.gro.1#
>>
>> Steepest Descents converged to machine precision in 15 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy  =  9.0435262e+19
>> Maximum force =inf on atom 2781
>> Norm of force =inf
>>
>>
>> The reason behind this was that DHB molecules were on top of each other,
>> highly dense system ( viewed in VMD)
>> So, to reduce the density of DHB molecules, I tried using-vdwd option of
>> genbox (changed from default value of 0.105 to 0.5)
>> But, I got almost same number of DHB molecules using genbox.
>>
>>
> The -vdwd option has no effect unless you're using atom names that are not
> found in vdwradii.dat (see the genbox help description).  Your DHB molecule
> should be unaffected by the use of -vdwd.
>
>
>
>> What is the best solution to this problem as I understand, reducing the
>> density of DHB molecules around the protein as a solvent or there is some
>> other problem?
>>
>>
> You need to generate a configuration in which molecules aren't overlapping.
> There are several ways to accomplish this.  You can manually place molecules
> within a box at a desired location with editconf -center, otherwise genbox
> -ci -nmol.  If the locations of the molecules are not what you desire with
> genbox, change the value of -seed and try again.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/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
>
-- 
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

[gmx-users] Questions about GB parameters

[Justin A. Lemkul]

Hi All,

I wanted to dig up an old discussion that hit the list a long time ago because 
I'm now encountering some problems understanding the GB settings myself.  The 
discussion in question is here:


http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html

I wanted to post a couple of questions based on Per's response.

1. Based on that post, it seems to me that the value in the gbr column should 
have a dielectric offset added to it during the GB calculations.  In the code, 
though (genborn.c, around line 484 in the latest release-4-5-patches), it looks 
like the dielectric offset is subtracted, not added.  I guess the code is 
reversing the process, going from GB radius back to vdW radius by subtracting 
the dielectric offset?  It seems, then, that the parameters in gbsa.itp should 
specify GB radii, not vdW radii, though the manual says the gbr column is 
"atomic van der Waals radii, which are used in computing the Born radii."  Is 
the opposite actually true?


2. I am still unclear on the source of the HCT scaling factors.  From the 
reference cited in the manual, it would seem that scaling factors are 
interaction-dependent, at least when H atoms are concerned.  I also cannot find 
any indication of where these values came from.  None of the values of Table 2 
in the HCT reference match the contents of the "hct" column.  Again I wonder if 
I'm missing something obvious :)


Thanks for any insight!

-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

Re: [gmx-users] mdrun -nc

[Joshua L. Phillips]

On most of my multi-core machines, an attempt is made to detect the
number of threads to start at run-time (there may be a check for the
MAXIMUM number of threads at compile-time, but a developer would need to
chime in to determine if this is the case). For instance, I have a dual
quadcore machine (eight cores total). When I just run a command like so
on 4.5.4:

mdrun -v -deffnm trp-cage

I get:

Starting 8 threads
Loaded with Money

Making 2D domain decomposition 4 x 2 x 1
starting mdrun 'Good ROcking Metal Altar for Chronical Sinners in water'
10 steps,200.0 ps.
step 200, will finish Tue Jun 14 12:01:01 2011imb F  8% 
...

So, by default the threaded version will start the maximum number of
threads that it can (if it can find a good decomposition for all cores,
otherwise fewer threads are used). So, -nt is used to explicitly control
the number of threads used (not -nc).

As Justin said, for running across multiple machines, MPI is necessary
and precludes using threads.

-- Josh

On Tue, 2011-06-14 at 11:15 -0400, Justin A. Lemkul wrote:
> 
> Hsin-Lin Chiang wrote:
> > Hi,
> > 
> > I tried gromacs 4.5.4 in these days and last version I used is 4.0.5.
> > I found when I add --enable-threads in installation.
> > I can use mdrun -nc 12 to run 12 CPUs together within one machine.
> 
> I assume you mean -nt?
> 
> > It also amazing me when I type "top" to check the job, only one process 
> > in computer and the CPU utility is 1200%!!
> 
> Sounds about right.  I see the same on my dual-core workstation.  One 
> process, 2 
> threads, and just less than 200% CPU usage.
> 
> > But I tried to execute it on two machines, then the second machines 
> > didn't work.
> > 
> 
> You can't execute threads over multiple machines.  For that you need MPI, not 
> threading (they are mutually exclusive).  You haven't provided much detail on 
> what you actually did in this case and "didn't work" doesn't exactly provide 
> any 
> relevant diagnostic information.
> 
> > I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi.
> > That make me confused.
> > Am I right to use mdrun -nc to run parallel job in this way?
> 
> For a single, multi-core workstation, mdrun -nt is correct.
> 
> > Does the result is the same as which is employed by mdrun_mpi?
> 
> A variety of factors influence whether or not the results are the same.
> 
> http://www.gromacs.org/Documentation/Terminology/Reproducibility
> 
> > (Exactly I never use mdrun_mpi more than one machine since the ethernet 
> > between machines is very slow here.)
> > 
> > If mdrun -nc is available.
> > Do we have another commend support CPUs more than one in the same machine.
> > 
> 
> That's what threading is doing, assuming you're invoking the command 
> correctly. 
>   As stated above, the option is -nt, not -nc.  mdrun doesn't check for 
> whether 
> or not command line arguments are actually valid, so if you're using -nc 
> you're 
> not actually doing threading, but the 1200% usage suggests you probably are.
> 
> -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
> 
> 

-- 
Joshua L. Phillips
Ph.D. Candidate - School of Engineering
University of California, Merced
jphilli...@ucmerced.edu


-- 
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

Re: Re: [gmx-users] Water Potential Energy

[Rini Gupta]

Dear Mark,

 Thanks for the reply!

I am using the same NPT conditions except time constants. 
The simulation was performed at constant temperature (300K) 
and pressure(1 bar) using velocity rescaling algorithm (tau=0.1 ps) 
for temperature coupling and Berendsen coupling 
scheme (tau=1 ps) for pressure coupling whereas the in the references the 
system was coupled to bath of constant temperature (300K) and pressure (1 bar) 
using time constants tau=0.4 ps for temperature coupling and taup=0.4 ps for 
pressure coupling.
Does it is making difference in calculated and reported values?
I am using LINCS algorithm to keep the geometries of all the molecules 
rigid. Other conditions are exactly same.
 
To see the size effect on the system,
I have also done the same calculations with 8000 molecules but result is same 
i.e. Water P.E=-46.7 kJ/mol.

Please clarify this issue.

Best Regards,
Rini

On Tue, 14 Jun 2011 08:13:39 +0530  wrote
>On 14/06/2011 4:18 AM, Rini Gupta wrote:

> Dear gmx-users,

>

> I am using GROMACS 4.5.4 to run a pure water system using SPC/E model

> containing 32000 molecules. I have done the equilibration for 2 ns 

> followed by production run of 5 ns using NPT ensemble at 300K.

> I am using PME for treating electrostatic interactions (cut-off 0.9 nm).

> My question is Potential Energy of the system I am getting is -46.7 

> kJ/mol while literature value is -41.5 kJ/mol.

> Can anyone please tell me why this discrepancy is coming?



PE is size- and method-dependent. Are you reproducing the conditions 

exactly?



Mark

-- 

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

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

Please search the archive at 
http://www.gromacs.org/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
-- 
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

Re: [gmx-users] Questions about GB parameters

[Per Larsson]

Hi!

Hmm.. Let me see if I can shed some more light on this. It's been a while 
though since I visited the literature here, and also my laptop broke down 
today, so I need to take of that first before I can check the code!

Thanks
/Per


14 jun 2011 kl. 20:24 skrev "Justin A. Lemkul" :

> 
> Hi All,
> 
> I wanted to dig up an old discussion that hit the list a long time ago 
> because I'm now encountering some problems understanding the GB settings 
> myself.  The discussion in question is here:
> 
> http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html
> 
> I wanted to post a couple of questions based on Per's response.
> 
> 1. Based on that post, it seems to me that the value in the gbr column should 
> have a dielectric offset added to it during the GB calculations.  In the 
> code, though (genborn.c, around line 484 in the latest release-4-5-patches), 
> it looks like the dielectric offset is subtracted, not added.  I guess the 
> code is reversing the process, going from GB radius back to vdW radius by 
> subtracting the dielectric offset?  It seems, then, that the parameters in 
> gbsa.itp should specify GB radii, not vdW radii, though the manual says the 
> gbr column is "atomic van der Waals radii, which are used in computing the 
> Born radii."  Is the opposite actually true?
> 
> 2. I am still unclear on the source of the HCT scaling factors.  From the 
> reference cited in the manual, it would seem that scaling factors are 
> interaction-dependent, at least when H atoms are concerned.  I also cannot 
> find any indication of where these values came from.  None of the values of 
> Table 2 in the HCT reference match the contents of the "hct" column.  Again I 
> wonder if I'm missing something obvious :)
> 
> Thanks for any insight!
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/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
--
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

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

[shivangi nangia]

Dear Justin,

I have run into another problem.

I created the system by including DHB in vwdradii.dat as follows:

; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.
; longest matches are used
; '???' or '*' matches any residue name
; 'AAA' matches any protein residue name
???  C 0.15
???  F 0.12
???  H 0.04
???  N 0.110
???  O 0.105
???  S 0.16
*DHB  C 0.5
DHB  H 0.5
DHB  O 0.5*
; Water charge sites
SOL  MW0
SOL  LP0
; Masses for vsite construction
GLY  MN1   0
GLY  MN2   0
ALA  MCB1  0
ALA  MCB2  0
VAL  MCG1  0
VAL  MCG2  0
ILE  MCG1  0
ILE  MCG2  0
ILE  MCD1  0
ILE  MCD2  0
LEU  MCD1  0
LEU  MCD2  0
MET  MCE1  0
MET  MCE2  0
TRP  MTRP1 0
TRP  MTRP2 0
THR  MCG1  0
THR  MCG2  0
LYSH MNZ1  0
LYSH MNZ2  0

After making this change, DHB molecules were not over lapping with each
other.

I tried to energy minimized the system.
minim.mdp
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent minimization)
;emtol= 1000.0; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1  ; Frequency to update the neighbor list and long range
forces
ns_type = grid  ; Method to determine neighbor list (simple, grid)
rlist= 1.0; Cut-off for making neighbor list (short range forces)
coulombtype = PME; Treatment of long range electrostatic interactions
rcoulomb = 1.0; Short-range electrostatic cut-off
rvdw = 1.0; Short-range Van der Waals cut-off
pbc  = xyz   ; Periodic Boundary Conditions (yes/no)
constraints = none


 After about 6000 steps the run stops with the message:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.

Steepest Descents converged to machine precision in 6012 steps,
but did not reach the requested Fmax < 10.
Potential Energy  =  1.0655116e+05
Maximum force =  1.6512177e+02 on atom 2076
Norm of force =  6.5337501e+00



The potential energy is high, but I still continued to equilibration.
After NVT equilibration, NVT equilbration runs into the following error as
soon it starts:


Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which is
larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
/var/spool/pbs/mom_priv/jobs/1869547.lionxj.rcc.psu.edu.SC: line 14:  2359
Segmentation fault  mdrun -deffnm npt




So, I have three questions:

1. Is the starting structure bad?
2. Did I change the vdwd radii by a lot (0.105 to 0.5)
3. What value of table extension should be used for 1-4 interaction (
default value is?) if thats the problem to be fixed.

Please guide.

Thanks,
SN




On Tue, Jun 14, 2011 at 11:29 AM, shivangi nangia  wrote:

> Thanks Justin, vdwradii.dat suggestion worked :)
>
>
>
>
> On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul wrote:
>
>>
>>
>> shivangi nangia wrote:
>>
>>> Hello dear gmx-users,
>>>
>>> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as
>>> the solvent ( with a positively charged protein and few DHB anions) in a
>>> box.
>>>
>>> I have created the .itp and .gro file of DHB using PRODRG.
>>>
>>>
>> Unrelated advice - the topology is probably useless unless you've
>> corrected the charges.  See the paper linked from:
>>
>> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>>
>>
>>  I am able to create the system, but when I try to energy minimize the
>>> system I get the message:
>>>
>>> Steepest Descents:
>>>   Tolerance (Fmax)   =  1.0e+01
>>>   Number of steps=5
>>> Step=   14, Dmax= 1.2e-06 nm, Epot=  9.04353e+19 Fmax= inf, atom=
>>> 2781
>>> Stepsize too small, or no change in energy.
>>> Converged to machine precision,
>>> but not to the requested precision Fmax < 10
>>>
>>> Double precision normally gives you higher accuracy.
>>>
>>> writing lowest energy coordinates.
>>>
>>> Back Off! I just backed up em.gro to ./#em.gro.1#
>>>
>>> Steepest Descents converged to machine precision in 15 steps,
>>> but did not reach the requested Fmax < 10.
>>> Potential Energy  =  9.0435262e+19
>>> Maximum force =inf on atom 2781
>>> Norm of force =inf
>>>
>>>
>>> The reason behind this was that DHB molecules were on top of each other,
>>> highly dense system ( viewed in VMD)
>>> So, to reduce the density of DHB molecules, I tried using-vdw

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

[Justin A. Lemkul]

shivangi nangia wrote:

Dear Justin,

I have run into another problem.

I created the system by including DHB in vwdradii.dat as follows:

; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.
; longest matches are used
; '???' or '*' matches any residue name
; 'AAA' matches any protein residue name
???  C 0.15
???  F 0.12
???  H 0.04
???  N 0.110
???  O 0.105
???  S 0.16
*DHB  C 0.5
DHB  H 0.5
DHB  O 0.5*
; Water charge sites
SOL  MW0
SOL  LP0
; Masses for vsite construction
GLY  MN1   0
GLY  MN2   0
ALA  MCB1  0
ALA  MCB2  0
VAL  MCG1  0
VAL  MCG2  0
ILE  MCG1  0
ILE  MCG2  0
ILE  MCD1  0
ILE  MCD2  0
LEU  MCD1  0
LEU  MCD2  0
MET  MCE1  0
MET  MCE2  0
TRP  MTRP1 0
TRP  MTRP2 0
THR  MCG1  0
THR  MCG2  0
LYSH MNZ1  0
LYSH MNZ2  0

After making this change, DHB molecules were not over lapping with each 
other.


I tried to energy minimized the system.
minim.mdp
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent minimization)
;emtol= 1000.0; Stop minimization when the maximum force < 
1000.0 kJ/mol/nm

emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions
nstlist = 1  ; Frequency to update the neighbor list and long 
range forces

ns_type = grid  ; Method to determine neighbor list (simple, grid)
rlist= 1.0; Cut-off for making neighbor list (short range forces)
coulombtype = PME; Treatment of long range electrostatic interactions
rcoulomb = 1.0; Short-range electrostatic cut-off
rvdw = 1.0; Short-range Van der Waals cut-off
pbc  = xyz   ; Periodic Boundary Conditions (yes/no)
constraints = none


 After about 6000 steps the run stops with the message:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.

Steepest Descents converged to machine precision in 6012 steps,
but did not reach the requested Fmax < 10.
Potential Energy  =  1.0655116e+05
Maximum force =  1.6512177e+02 on atom 2076
Norm of force =  6.5337501e+00



The potential energy is high, but I still continued to equilibration.
After NVT equilibration, NVT equilbration runs into the following error 
as soon it starts:



Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which 
is larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
/var/spool/pbs/mom_priv/jobs/1869547.lionxj.rcc.psu.edu.SC 
: line 14:  2359 Segmentation 
fault  mdrun -deffnm npt





So, I have three questions:

1. Is the starting structure bad?


Probably.


2. Did I change the vdwd radii by a lot (0.105 to 0.5)


Yes.  And you shouldn't use those artificial values for anything else.  Remove 
them after you've inserted the DHB into your system.  This is, of course, no 
guarantee that the system is stable, either.


3. What value of table extension should be used for 1-4 interaction ( 
default value is?) if thats the problem to be fixed.




Do not adjust the table extension.  If the system is blowing up, there's no 
reason to troubleshoot the constraints; they're not your problem.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

[gmx-users] Question about umbrella sampling through a nanotube

[WU Yanbin]

Dear GMXers,

I'm trying to compute the PMF of a molecule along the centerline of a
nanotube (the axial direction of the nanotube is parallel to the z axis).
The nanotube is used as the reference group and the molecule as the pulling
group.

pull_geometry   = position
pull_dim= Y Y Y
pull_start  = no
pull_init1  = 0 0 1.2
pull_rate1  = 0.00
pull_k1 = 1000
pull_nstxout= 1000
pull_nstfout= 1000


"pull_dim=Y Y Y" is used to make sure that the molecule is always close to
the centerline of the nanotube.
>From the output of "pullx.xvg", the COM positions in all three directions
(i.e. x,y,z) are included.
How to get the PMF only along z axis from here? Is it OK if I just take the
corresponding z column and do g_wham directly?

Thank you.

Best,
Yanbin
-- 
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

[gmx-users] Question about umbrella sampling through a nanotube

[chris . neale]

Unfortunately, I don't think that there is any way to use this data  
(and only this data) to derive the PMF along z. The way that you did  
your US, the PMF along z is convoluted with xy motion. You can get the  
PMF along the reaction coordinate that you actually used (XYZ) using  
standard WHAM and try to interpret it, I suppose. In your special  
case, there is probably a mathematical conversion between the XYZ PMF  
and the Z-only PMF due to the symmetry of the system.


What one would desire is two separate restraints, one operating in Z  
and one operating in XY. That is, unfortunately, not possible in the  
standard version of gromacs.


-- original message --

Dear GMXers,

I'm trying to compute the PMF of a molecule along the centerline of a
nanotube (the axial direction of the nanotube is parallel to the z axis).
The nanotube is used as the reference group and the molecule as the pulling
group.

pull_geometry   = position
pull_dim= Y Y Y
pull_start  = no
pull_init1  = 0 0 1.2
pull_rate1  = 0.00
pull_k1 = 1000
pull_nstxout= 1000
pull_nstfout= 1000


"pull_dim=Y Y Y" is used to make sure that the molecule is always close to
the centerline of the nanotube.

From the output of "pullx.xvg", the COM positions in all three directions

(i.e. x,y,z) are included.
How to get the PMF only along z axis from here? Is it OK if I just take the
corresponding z column and do g_wham directly?

Thank you.

Best,
Yanbin
-- next part --


--
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

[gmx-users] simulating a protein homodimer

[Stephen Edgcomb]

Hello All

I am trying to simulate a protein homodimer.

My command lines are:

pdb2gmx -f dimer.pdb -p dimer.top -o dimer.gro -ignh -ter -chainsep
interactive

grompp -f minim.mdp -c dimer.gro -p dimer.top -o input.tpr

mdrun -nice 0 -v -s input.tpr -o minim_traj.trr -c minimized.gro -e
minim_ener.edr

editconf -f minimized.gro -o mdrundimer.pdb



the mdrun step results in the second chain of the dimer translocated away
from the first chain.  I do not know what is causing the translocation.  The
dimer should just be completing a gas phase equilibration.





Any help would be appreciated, and please let me know if more information is
required to answer my question.

Thank you,

Steve
-- 
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

Re: [gmx-users] simulating a protein homodimer

[Justin A. Lemkul]

Stephen Edgcomb wrote:

Hello All

I am trying to simulate a protein homodimer.

My command lines are:

pdb2gmx -f dimer.pdb -p dimer.top -o dimer.gro -ignh -ter -chainsep 
interactive


grompp -f minim.mdp -c dimer.gro -p dimer.top -o input.tpr

mdrun -nice 0 -v -s input.tpr -o minim_traj.trr -c minimized.gro -e 
minim_ener.edr


editconf -f minimized.gro -o mdrundimer.pdb

 

the mdrun step results in the second chain of the dimer translocated 
away from the first chain.  I do not know what is causing the 
translocation.  The dimer should just be completing a gas phase 
equilibration.


 


Energy minimization should not result in any large-scale movement of the 
protein.  Sounds like a classic case of PBC:


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin



 

Any help would be appreciated, and please let me know if more 
information is required to answer my question. 

Thank you, 


Steve



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

[gmx-users] trjconv with superposition

[Liu Shiyong]

Dear Colleagues,

I want to extract PDB snapshot from trajectory file by following command. It
works in 4.0, but not in 4.5

pdb=1akk
trjconv -f ${pdb}_gromos53a6_MD2.traj.trr -o ${pdb}_gromos53a6_MD2.traj.xtc

trjconv -s ${pdb}_gromos53a6_MD2.tpr -f ${pdb}_gromos53a6_MD2.traj.xtc -dt
20 -b 0 -o ${pdb}_gromos53a6_MD2.traj.nojump.pdb -fit rot+trans -pbc nojump


Program trjconv, VERSION 4.5.3
Source code file: gmx_trjconv.c, line: 854

Fatal error:
PBC condition treatment does not work together with rotational fit.
Please do the PBC condition treatment first and then run trjconv in a second
step
for the rotational fit.
First doing the rotational fit and then doing the PBC treatment gives
incorrect
results!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Best

Shiyong

-- 
Shiyong Liu
--
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-805
--
Chinese Version:
--
刘士勇
华中科技大学物理学院  生物物理模建小组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-805
---
-- 
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

Re: [gmx-users] trjconv with superposition

[Justin A. Lemkul]

Liu Shiyong wrote:
Dear Colleagues, 

I want to extract PDB snapshot from trajectory file by following 
command. It works in 4.0, but not in 4.5
 
pdb=1akk

trjconv -f ${pdb}_gromos53a6_MD2.traj.trr -o ${pdb}_gromos53a6_MD2.traj.xtc

trjconv -s ${pdb}_gromos53a6_MD2.tpr -f ${pdb}_gromos53a6_MD2.traj.xtc 
-dt 20 -b 0 -o ${pdb}_gromos53a6_MD2.traj.nojump.pdb -fit rot+trans -pbc 
nojump



Program trjconv, VERSION 4.5.3
Source code file: gmx_trjconv.c, line: 854

Fatal error:
PBC condition treatment does not work together with rotational fit.
Please do the PBC condition treatment first and then run trjconv in a 
second step

for the rotational fit.
First doing the rotational fit and then doing the PBC treatment gives 
incorrect

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



This is one of the more explicit and helpful error messages.  It tells you why 
you can't do what you want and also tells you exactly how to fix it.  Doing 
fitting and PBC correction in one trjconv command may have "worked" in a 
previous version, but it's never been correct to do so.


-Justin



Best

Shiyong

--
Shiyong Liu
--
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-805
--
Chinese Version:
--
刘士勇
华中科技大学物理学院  生物物理模建小组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-805
---



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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

[gmx-users] g_density

[Matthias Schmidt]

Hi,

I have aligned a trajectory to a reference structure and have now run
g_density on both the original and the aligned trajectory in order to
find the bilayer headgroup position and the bilayer thickness.

g_density works fine with the original trajectory but there seems to
be a bug when running it to the aligned structure (Alignment done
using trjconv -fit progressive).

The density is calculated along the z direction (-d Z). The density
for positive z is calculated correctly, but the density for negative z
is shifted about 15nm to to the top end of the box size, as if the
density distribution along the z-axis were discontinuous.

Other then stitching the data together by hands, are there any obvious
better solutions?

Thanks,

Matthias
-- 
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

[gmx-users] Re: mdrun -nc

[Hsin-Lin Chiang]

>/  Hi,
/>/
/>/  I tried gromacs 4.5.4 in these days and last version I used is 4.0.5.
/>/  I found when I add --enable-threads in installation.
/>/  I can use mdrun -nc 12 to run 12 CPUs together within one machine.
/
I assume you mean -nt?


Sorry, -nc is a typo of -nt.

>/  It also amazing me when I type "top" to check the job, only one process
/>/  in computer and the CPU utility is 1200%!!
/
Sounds about right.  I see the same on my dual-core workstation.  One process, 2
threads, and just less than 200% CPU usage.

>/  But I tried to execute it on two machines, then the second machines
/>/  didn't work.
/>/
/
You can't execute threads over multiple machines.  For that you need MPI, not
threading (they are mutually exclusive).  You haven't provided much detail on
what you actually did in this case and "didn't work" doesn't exactly provide any
relevant diagnostic information.

If I submit job by the way, mdrun -nt 24, on two machines with 12 threads for 
each.
The first machine has one process with 1200%, and the second machine has no 
process working.

>/  I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi.
/>/  That make me confused.
/>/  Am I right to use mdrun -nc to run parallel job in this way?
/
For a single, multi-core workstation, mdrun -nt is correct.

Thank you for you answer, then I can feel easy in mind to use this argument, 
-nt.
And also thanks for Phillips's reply.
I understand it now.

Hsin-Lin

>/  Does the result is the same as which is employed by mdrun_mpi?
/
A variety of factors influence whether or not the results are the same.

http://www.gromacs.org/Documentation/Terminology/Reproducibility

>/  (Exactly I never use mdrun_mpi more than one machine since the ethernet
/>/  between machines is very slow here.)
/>/
/>/  If mdrun -nc is available.
/>/  Do we have another commend support CPUs more than one in the same machine.
/>/
/
That's what threading is doing, assuming you're invoking the command correctly.
   As stated above, the option is -nt, not -nc.  mdrun doesn't check for whether
or not command line arguments are actually valid, so if you're using -nc you're
not actually doing threading, but the 1200% usage suggests you probably are.

-Justin


-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/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