[gmx-users] About densmap tool

[Yasser Almeida Hernández]

Hello,

I am working with a membrane protein inserted in a heterogeneous 
bilayer, with different lipids at different ratios. I used gmx densmap 
to obtain 2D maps of the lipids distribution, based in the PO4 group. I 
use the command as following:


gmx densmap -s  -f  -n  -od 
 -unit nm-2 -bin 0.1


Attached is one example of one of my raw output maps.

According with the command-line reference: "The normalization of the 
output is set with the -unit option. The default produces a true number 
density. Unit nm-2 leaves out the normalization for the averaging or the 
angular direction. Option count produces the count for each grid cell. 
When you do not want the scale in the output to go from zero to the 
maximum density, you can set the maximum with the option -dmax."


I am not sure if I am interpreting the results in a proper way.

1 - If "Unit nm-2 leaves out the normalization for the averaging or the 
angular direction", what do the numbers in the output file actually mean?


2 - Are they the average in each grid point, along the whole simulation 
time?


3 - It may sound as a silly question, but how does this command define 
"density"?


Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] CG lipid diffusion coefficient

[Yasser Almeida Hernández]

Hi all,

I ran some CG simulations of a protein inserted in a lipid bilayer, with 
several lipids. I used the msd tool to compute the lipid (using the PO4) 
diffusion coefficient. For one of the lipid I got D = 0.6 x 10^-5 
cm^2/s, which is 600 um^2/s. According to the Martini website "To 
compare the diffusion coefficient obtained from a Martini simulation to 
a measured one, a conversion factor of about 4 has to be applied to 
account for the faster diffusion at the CG level due to the smoothened 
free energy landscape (note, the conversion factor can vary 
significantly depending on the molecule in question)." (J Phys Chem B. 
2009 Feb 5; 113(5): 1501–1510.)


The value I get is 2 orders of magnitude higher of a comparable value of 
6 um^2/s.


Would this make sense?

Regards

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Help with gmx select

[Yasser Almeida Hernández]

Hello,

I want to use gmx select to get a list of protein residues that interact 
with PO4 beads (CG) in a bilayer: The command I am using is:


gmx select -s system.gro -f traj.xtc -oi contacting_residues_DOPG.dat 
-resnr number -n PO4_index_1.ndx -select 'group Protein and same residue 
as within 0.6 of (group PO4_DOPG_upper or group PO4_DOPG_lower)'


But it returns the list of all atoms numbers of every interacting 
residue. I want ONLY the residue number.


Any idea?

Thanks in advance

Yasser


--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] contacts

[Yasser Almeida Hernández]

Hello,

I did a CGMD run of a membrane protein embedded in a model bilayer and I 
want to compute the contacts between my protein and the PO4 beads of 
certain lipid. I am using the following command:


gmx mindist -s md_protein_membrane_1.tpr -f 
md_protein_membrane_centered_run1.xtc -or mindistres_1.xvg -od 
mindist_1.xvg -o atm-pair_1.out -on numcont_1.xvg -tu ns -d 0.6 -n index.ndx


Then, I got the output in the numcont.xvg and atm-pair.out:


9.00e+03 6
9.11e+03 5
9.21e+03 6
9.30e+03 3
9.40e+03 6
9.51e+03 3
9.61e+03 1
9.70e+03 1
9.80e+03 1
9.91e+03 2
9.000101e+03 2
9.000110e+03 1
...


9.00e+03   285  5019
9.11e+03   286  5019
9.21e+03   284  5019
9.30e+03   293  5019
9.40e+03   293  5019
9.51e+03   299  5151
9.61e+03   299  5151
9.70e+03   293  5019
9.80e+03   293  5019
9.91e+03   293  5019
9.000101e+03   293  5019
9.000110e+03   299  5151
...

If I interpret correctly (please correct me if I am wrong), numcont.xvg 
informs that -for example- at time 9.00e+03 there are 6 contacts, 
but then in atm-pair.out at that time there are 1 contact between 
atom/bead 285 and 5019. Do I am missing something?


At the end what I want is to get per-residue contacts between the 
protein and the PO4 beads, to map them on the protein to see which 
region have more contacts.


Thanks in advance.

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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Re: [gmx-users] Temperature in CG production runs

[Yasser Almeida Hernández]

The reference temperature depends on what you want to model, and how
well the force field reproduces the phase transition temperature of the
lipids. If, for example, the force field requires higher temperature for
a lipid type to remain liquid crystalline than it should, you have to
decide if the higher temperature is reasonable or if you should be using
a different force field that is more accurate.

-Justin


What I want to model is the diffusion of several lipids, in interaction 
of a membrane protein. Buslaev and Gushchin 
(https://www.nature.com/articles/s41598-017-11761-5) simulated lipids at 
different temperatures using different FFs, showing little differences. 
In my case I have a bilayer with DPPE, DOPE, POPE, DPPG, DOPG, POPG and 
CDL, plus a membrane protein, so I think regular physiological 310K is 
the best, right?


Best

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Temperature in CG production runs

[Yasser Almeida Hernández]

Dear all,

I am performing CG simulations (Martini) of a membrane protein in an 
heterogeneous model bilayer with several lipids, resembling the inner 
membrane from E. coli.


Looking in the literature, I have seen that the temperature for 
production runs range from 300-330K, which are a big difference in 
physiological terms. What temperature would you recommend in my case?


Thanks in advance and best regards

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Coordinates transformation

[Yasser Almeida Hernández]

Hi all,

I have two different simulations of a membrane protein in a E. coli 
model membrane, and I want to analyze the protein-lipids interactions, 
by generating 2D density maps. In each simulation, the protein 
moves/rotates different along the xy plane of the membrane, and ends up 
in a different orientation.


Is there a way to transform the coordinates of one simulation, ex. 
superposing one onto the other (taking the protein coordinates of the 
first simulation as reference) to have both in the same coordinates 
system and the proteins in the same orientation, so I can generate 
comparable 2D maps?


Thanks in advance.

Regards

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Membrane simulation analysis - membrane thickness and area per lipid

[Yasser Almeida Hernández]

Hello,

I am running some CGMD simulations of a membrane protein embedded in a 
model of E. coli membrane (12x12 nm bilayer with different lipids), and 
I want to do the analysis of the membrane thickness and area per lipid 
(APL). For these tasks I am comparing the performance of FATSLiM, 
APL@Voro, GridMAT-MD and the GROMACS tool densmap. For this I have 
several questions:


1 - I am running densmap as *gmx densmap -f traj.xtc -s topol.tpr -n 
PO4_index.ndx -od densmap.dat* selecting the lipid of interest (as the 
PO4 bead), previously grouped in the index file. Then I plotted the 
*densmap.dat* file in Origin, obtaining a color coded heatmap of each 
lipid for the upper and lower membrane leaflet. What are the unit for 
this density maps? The *-unit* options are in nm-3, nm-2 or count. If I 
select *-unit nm-2*, does that means number of lipids per nm-2?


2 - How different is the previous approach from the APL calculated in 
FATSLiM, APL@Voro, GridMAT-MD?


3 - Which is the best method for the membrane thickness calculation.

Thanks

Best

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] 2D density maps

[Yasser Almeida Hernández]

Hello,

I am running simulations of a membrane protein embedded in a E. coli 
model membrane. I want to generate 2D density plots to visualize lipids 
clustering and interaction with the protein, and membrane thickness. 
Which tool would you recommend? I have seen the tools from Luca 
Monticelli web site, reported in 
https://www.sciencedirect.com/science/article/pii/S0009308413000236?via%3Dihub.


Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Water tracking along simulation

[Yasser Almeida Hernández]

Hello everyone,

It is any tool to track water molecules (or a particle in general) along 
a simulation trajectory, so the final result is the pathway/streamline 
of selected water molecules? It would something similar to what was done 
in this paper http://pubs.acs.org/doi/abs/10.1021/bi901900s.


Thanks in advance.

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] 2D maps

[Yasser Almeida Hernández]

Hello all,

I have CGMD simulation for a membrane protein embedded in a model 
membrane with several E. coli lipids, built with /insane/ script. I want 
to generate colored scaled 2D maps for the membrane thickness and for 
the lipids distributions for each bilayer leaflet. Could you give some 
guidelines in this regard?


Thanks in advance

Best regards

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Running GROMACS on cluster

[Yasser Almeida Hernández]

Hi all,

I am strugling to run GROMACS on a cluster with SGE queue system, but I 
have any acceleration. The verbose output says that it will end is 
September 2017!!. This is the script I am using to run.



#!/bin/bash
#$ -cwd
#$ -pe parallel 24
#$ -q main.q  #name of the queue
#$ -e stderr.log   # redirections for stdout,err
#$ -o stdout.log

#export LD_LIBRARY_PATH=/home/whoever/mylibdir:$LD_LIBRARY_PATH
# any changes you need to the environment

#MPIRUN=$I_MPI_ROOT/intel64/bin/mpirun # this is the full path to the 
correct mpirun installation.
#OPENMPI=/opt/openmpi-1.8.1/bin/mpirun -mca btl ^usnic -machinefile 
hosts -np $NSLOTS # this is the full correct command for open-mpirun

#CMD=mdrun_mpi -v -deffnm md_glpg_NG_50ns # command to be executed

export I_MPI_FABRICS=shm:ofa

mpirun /usr/bin/mdrun_mpi -v -deffnm md_protein_NG_100ns_packmol



My system is composed by a membrane protein, detergent, water and ions.

Thanks in advance

Yasser


--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Segmentation fault error during run

[Yasser Almeida Hernández]

Hi all,
I am simulating a solvated system with a membrane protein and detergent 
NG (beta-nonylgrucoside), using GROMACS 4.6.5. I got the topology for NG 
from ATB database. During the simulation I got this Segmentation fault 
error:



(...)
Step 173550, time 347.1 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.170158, max 8.399462 (between atoms 2306 and 2307)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2306   2307   90.30.1267   1.0527  0.1120
   2306   2308   38.00.1532   0.1445  0.1530
   2306   2311   80.80.1534   0.2344  0.1530
   2311   2312   89.40.1131   0.1629  0.1130
   2311   2313   86.80.1423   0.2395  0.1420
   2311   2315   49.10.1535   0.2080  0.1530
   2313   2314   52.30.0972   0.1227  0.0971
   2315   2316   57.50.1131   0.1533  0.1130
   2315   2317   50.10.1422   0.1846  0.1420
   2315   2319   47.70.1532   0.1994  0.1530
   2317   2318   37.80.0971   0.1220  0.0971
Wrote pdb files with previous and current coordinates

Step 173551, time 347.102 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.093200, max 4.227952 (between atoms 2306 and 2307)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2305   2306   53.70.1182   0.1114  0.1430
   2306   2307   88.01.0527   0.5855  0.1120
   2306   2308   64.10.1445   0.1706  0.1530
   2308   2309   34.50.1495   0.1514  0.1420
   2309   2310   40.20.0978   0.1113  0.0971
   2311   2312   94.20.1629   0.3210  0.1130
   2311   2313   75.60.2395   0.1580  0.1420
   2313   2314   62.00.1227   0.1386  0.0971
   2315   2317   59.20.1846   0.1394  0.1420
   2315   2319   37.00.1994   0.1497  0.1530
   2317   2318   35.80.1220   0.1015  0.0971
Wrote pdb files with previous and current coordinates

Step 173552, time 347.104 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 4885.612961, max 229375.093750 (between atoms 2317 and 2318)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2299   2300   31.30.1520   0.1785  0.1520
   2300   2301   76.40.1520   4.6510  0.1520
   2301   2302  142.50.1434  14.0997  0.1430
   2303   2304   75.30.1115 124.7837  0.1120
   2303   2305   82.30.1386 118.6994  0.1430
   2303   2319  125.80.1578 369.9674  0.1540
   2305   2306   83.40.1114  21.8297  0.1430
   2306   2307   83.90.5855  24.8837  0.1120
   2306   2308   72.20.1706  26.9393  0.1530
   2306   2311   65.90.1676 228.0349  0.1530
   2308   2309  143.20.1514   5.3767  0.1420
   2309   2310  136.90.1113   0.4643  0.0971
   2311   2312  123.40.3210 174.6479  0.1130
   2311   2313   97.10.1580 242.5305  0.1420
   2311   2315   83.10.1557 1329.8728  0.1530
   2313   2314   64.90.1386   4.5339  0.0971
   2315   2316   87.60.0823 9123.7598  0.1130
   2315   2317   80.00.1394 1790.7780  0.1420
   2315   2319   64.00.1497 1212.5186  0.1530
   2317   2318   89.80.1015 22272.4199  0.0971
   2319   2321  129.10.1483 397.1000  0.1420
   2321   2322   45.00.0925 178.4549  0.0971
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 2298 and 2301
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


The system seems to be well equilibrated.

Any thoughts?

Thanks in advance.

Best

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Running GROMACS in cluster with SGE

[Yasser Almeida Hernández]

Hi all,

I am trying to run a simulation on a cluster with SGE queue system with 
this script:


***
#!/bin/bash
#$ -cwd
#$ -pe parallel 16 #number of cores
#$ -q main.q  #name of the queue
#$ -q mai...@xbes23.akbester.zz #one can choose particular node
#$ -e stderr.log   # redirections for stdout,err
#$ -o stdout.log

export I_MPI_FABRICS=shm:ofa

mpirun mdrun -v -deffnm sim1

***

For some reason I get a very poor performance around 0.8 ns/day in a 
node with 16 cores, compared with a workstation with 8 cores, where I 
get 2 ns/day.


I am running GROMACS 4.5.5 installed from the Ubuntu repository in each 
node. Could this be the reason for the poor performance?
Should I compile GROMACS from source code on the cluster (cluster 
optimized)?


Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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Re: [gmx-users] Adding detergent to simulation box - SOLVED

[Yasser Almeida Hernández]

I solved the problem adding NG, water and ions in that order.

Cheers

Yasser


On 10.01.2017 13:25, Yasser Almeida Hernández wrote:

Hello all,

I am trying to build a system containing a membrane protein, water, 
ions and NG detergent (beta-nonylglucoside). A conflict arise when I 
try to add NG and ions. If I build the system containing the protein, 
water and ions, and then add NG (with -ci and -nmol options of genbox 
command), none NG molecule is added. On the other hand if I build the 
solvated box with the protein and NG, and then add the ions, the NG 
molecules are destroyed/disordered and clustered in the box edges.


Any thoughts?

Thanks in advance

Yasser



--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Adding detergent to simulation box

[Yasser Almeida Hernández]

Hello all,

I am trying to build a system containing a membrane protein, water, ions 
and NG detergent (beta-nonylglucoside). A conflict arise when I try to 
add NG and ions. If I build the system containing the protein, water and 
ions, and then add NG (with -ci and -nmol options of genbox command), 
none NG molecule is added. On the other hand if I build the solvated box 
with the protein and NG, and then add the ions, the NG molecules are 
destroyed/disordered and clustered in the box edges.


Any thoughts?

Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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Re: [gmx-users] Box dimensions variation

[Yasser Almeida Hernández]

Hi Tsjerk,

Thanks! You are right. I used Pcoupltype = semiisotropic, so I should 
change it to isotropic.


Cheers

Yasser


Hi Yasser,

Probably you're using semi-isotropic pressure coupling, which you should
only do if you have a membrane like structure aligned with the XY plane (or
a somewhat stiffish wire like structure aligned along z).

Cheers,

Tsjerk


--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Box dimensions variation

[Yasser Almeida Hernández]

Hi all,
I have a coarse grained system (membrane protein/water/ions/polymer) in 
a 20 nm box, running during 2 us. During the run the box dimensions 
varies significantly, increasing in Z and decreasing in X and Y 
(identically) to almost the same XY dimensions of my protein.


Any ideas?

Thanks in advance

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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Re: [gmx-users] Laptop features for MD simulations - recommendations

[Yasser Almeida Hernández]

Hi Dries,

Let's say that the price is irrelevant right now. Just imagine an 
hardware with all the ideal features for the calculations.


Thanks all for your answers.

Best

Yasser


--

Hi Yasser,

Could you give us an idea of the price range you're looking at? I'd
probably try to get a laptop with a decent gpu to accelerate your work as
much as possible. Unfortunately, such laptops are often pricy.

Kind regards

Dries

On 3 February 2016 at 11:17, Yasser Almeida Hern?ndez <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:


Dear Joao,

I am aware that laptops are not the proper hardware to run MD simulations.
I do my runs in workstations designed for that purpose. The hardware I want
to buy is not just for simulations, but for general private/work purpose,
but I would like to have a device robust enough to run calculations. My
question was to get some thoughts about an ideal/optimal hardware.

Best

Yasser


Message: 6
Date: Wed, 3 Feb 2016 10:53:31 +0100
From: Jo?o Henriques 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Laptop features for MD simulations -
recommendations
Message-ID:
<
calc+hgt7zsmbkwitu11dprvh4m_qyw2btkgnsq2tvb70o71...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear Yasser,

I am by no means an expert on hardware, but I would strongly advise against
buying a laptop for the specific purpose of running (any and all) MD
simulations. A desktop is much better suited platform for such a task, as
you should be able to get a much bigger bang for your buck (this is the
main reason, but there are more cons).

Notice that I am not saying that you cannot run MD simulations on a laptop,
I'm just advising against it. In fact, you could probably run MD
simulations on a smartphone if you wanted to, but it doesn't sound like a
very good investment of your time and money. In my *personal opinion*, the
same holds true for the laptop.

Best regards,
/J

On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:

Hi all,


I want to buy a laptop suitable and powerful enough for MD simulations
with GROMACS (mostly membrane/protein systems). Could you recommend
optimal
features for this goal?

Thanks

Yasser

--
Yasser Almeida Hern?ndez
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c


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[gmx-users] Laptop features for MD simulations - recommendations

[Yasser Almeida Hernández]

Hi all,

I want to buy a laptop suitable and powerful enough for MD simulations 
with GROMACS (mostly membrane/protein systems). Could you recommend 
optimal features for this goal?


Thanks

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Laptop features for MD simulations - recommendations

[Yasser Almeida Hernández]

Dear Joao,

I am aware that laptops are not the proper hardware to run MD 
simulations. I do my runs in workstations designed for that purpose. The 
hardware I want to buy is not just for simulations, but for general 
private/work purpose, but I would like to have a device robust enough to 
run calculations. My question was to get some thoughts about an 
ideal/optimal hardware.


Best

Yasser


Message: 6
Date: Wed, 3 Feb 2016 10:53:31 +0100
From: Jo?o Henriques 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Laptop features for MD simulations -
recommendations
Message-ID:

Content-Type: text/plain; charset=UTF-8

Dear Yasser,

I am by no means an expert on hardware, but I would strongly advise against
buying a laptop for the specific purpose of running (any and all) MD
simulations. A desktop is much better suited platform for such a task, as
you should be able to get a much bigger bang for your buck (this is the
main reason, but there are more cons).

Notice that I am not saying that you cannot run MD simulations on a laptop,
I'm just advising against it. In fact, you could probably run MD
simulations on a smartphone if you wanted to, but it doesn't sound like a
very good investment of your time and money. In my *personal opinion*, the
same holds true for the laptop.

Best regards,
/J

On Wed, Feb 3, 2016 at 10:30 AM, Yasser Almeida Hern?ndez <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:


Hi all,

I want to buy a laptop suitable and powerful enough for MD simulations
with GROMACS (mostly membrane/protein systems). Could you recommend optimal
features for this goal?

Thanks

Yasser

--
Yasser Almeida Hern?ndez
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

--
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End of gromacs.org_gmx-users Digest, Vol 142, Issue 14
**



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[gmx-users] PBC in membrane protein system

[Yasser Almeida Hernández]

Hi all,

I am simulating a membrane protein in coarse-grained mode. The protein 
diffuse in the membrane and in the final frame my protein is in one of 
the box borders, so the coordinates are splitted to the opposite border 
(PBC). Then when I used backward.py to translate to all-atom 
coordinates, also results in splitted coordinates. I've tried several 
trjconv option with any success. How can I get the protein centered in 
the membrane?


Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] mdp files

[Yasser Almeida Hernández]

Hi all,

I am running CGMD simulation of a membrane protein in DPPC with Martini FF.

I just want to check if these mdp files are correct. I would appreciate 
if you take a look and tell me if there is something wrong or missing.


<*minimization.mdp*>
integrator   =  steep
dt   =  0.02
nsteps   =  500
nstxout  =  0
nstvout  =  0
nstlog   =  100
nstxtcout=  100
xtc-precision=  10
rlist=  1.4
coulombtype  =  shift
rcoulomb =  1.2
epsilon_r=  15
vdw-type =  shift
rvdw-switch  =  0.9
rvdw =  1.2
tcoupl   =  v-rescale
tc-grps  =  Protein DPPC W_Ion
tau-t=  1.0 1.0 1.0
ref-t=  300 300 300
define  = -DPOSRES

<*equilibration.mdp*>
dt   =  0.02
nsteps   =  25000
nstxout  =  0
nstvout  =  0
nstlog   =  100
nstxtcout=  100
xtc-precision=  100
rlist=  1.4
coulombtype  =  shift
rcoulomb =  1.2
epsilon_r=  15
vdw-type =  shift
rvdw-switch  =  0.9
rvdw =  1.2
tcoupl   =  v-rescale
tc-grps  =  Protein DPPC W_Ion
tau-t=  1.0 1.0 1.0
ref-t=  300 300 300
Pcoupl   =  parrinello-rahman
Pcoupltype   =  semiisotropic
tau-p=  12.0 12.0
compressibility  =  3e-4 3e-4
ref-p=  1.0 1.0
refcoord_scaling =  all

<*md_2us.mdp*>
dt   =  0.02
nsteps   =  1
nstxout  =  0
nstvout  =  0
nstlog   =  1
nstxtcout=  1000
xtc-precision=  100
rlist=  1.4
coulombtype  =  shift
rcoulomb =  1.2
epsilon_r=  15
vdw-type =  shift
rvdw-switch  =  0.9
rvdw =  1.2
tcoupl   =  v-rescale
tc-grps  =  Protein DPPC W_Ion
tau-t=  1.0 1.0 1.0
ref-t=  300 300 300
Pcoupl   =  parrinello-rahman
Pcoupltype   =  semiisotropic
tau-p=  12.0 12.0
compressibility  =  3e-4 3e-4
ref-p=  1.0 1.0

Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Custom elastic network of a membrane protein

[Yasser Almeida Hernández]

Hi all,

I am simulating a membrane protein in DPPC in order to insert it in the 
bilayer. I did a previous run during 2 us and I saw major changes in the 
secondary structure. Now I want to use an elastic network in order to 
preserve the overall secondary structure.


It is possible to build an elastic network, lets say the TM helices, 
excluding other parts of the protein, ej. soluble domains, with 
martinize.py (or any other tool)?


Thanks

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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Re: [gmx-users] Membrane protein insertion

[Yasser Almeida Hernández]

Thanks!

My protein is 200 amino acids single chain molecule. I tried the 
minimization in vacuo (potential.xvg), using the em.mdp file (see 
attached). I feel that the system is not really minimized. I check the 
pdb file and it seems ok. Shall I start again with the in vacuum 
minimized structure?


What do you think?

Best

Yasser

Am 24.08.2015 um 17:07 schrieb 
gromacs.org_gmx-users-requ...@maillist.sys.kth.se:

--

Message: 2
Date: Mon, 24 Aug 2015 12:33:08 +
From: Nash, Anthony a.n...@ucl.ac.uk
To: gmx-us...@gromacs.org gmx-us...@gromacs.org
Subject: Re: [gmx-users] Membrane protein insertion
Message-ID: d200cd32.56fb%ucca...@live.ucl.ac.uk
Content-Type: text/plain; charset=iso-8859-1

Hi,


I used this method recently and I was experiencing the same errors. As
Mark suggested, makes sure your protein survives an energy minimisation.
My error was a result of poor preparation of the .pdb file before running
pdb2gmx. My .itp file contained a long bond between the C and N termini of
a dimer.

IF you have any doubts, try running InflateGRO2 using a very small part of
your protein (1 chain) and see if it works.

Anthony

On 24/08/2015 08:59, Mark Abraham mark.j.abra...@gmail.com wrote:


Hi,

Something isn't stable. Check that your membrane protein survives a vacuum
EM (at least). And check your parameter settings for inflategro.

Mark

On Mon, Aug 24, 2015 at 9:53 AM Yasser Almeida Hern?ndez 
yasser.almeida.hernan...@chemie.uni-hamburg.de wrote:


Hi all,

I want to insert a membrane protein into a model bilayer and I've tried
several methods. The more straightforward seems to be Memembed, which
gives an orientation to the membrane. On the other hand this method only
outputs the membrane as dummy balls. How to translate this orientation
to a model bilayer (DOPC, POPC)?

On the other hand I've tried InflateGRO2 for this purpose and I got this
error (following the tutorial in
https://code.google.com/p/inflategro2/wiki/TutorialTolC ):

Back Off! I just backed up ../1-topology/4hzuS_popc.top to
../1-topology/#4hzuS_popc.top.3#
Will use a deflating factor of 0.925539817285086 to shrink the lipids
back in 20 steps
Deflating
grompp -f deflate.mdp -c inflated.gro -p ../1-topology/4hzuS_popc.top -n
inflated.ndx -o tmp.tpr -maxwarn 1
mdrun -s tmp.tpr -v -deffnm tmp_out -c shrink.00.gro
-
ERROR: Cannot open GRO file shrink.00.gro: No such file or directory


The end of the log.out file is this:

Fatal error:
Too many LINCS warnings (1184)
If you know what you are doing you can adjust the lincs warning
threshold in your mdp file or set the environment variable
GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem

Any thoughts?

Thanks in advance

--
Yasser Almeida Hern?ndez
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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--

Message: 3
Date: Mon, 24 Aug 2015 15:55:40 +0200
From: Andreas Mecklenfeld a.mecklenf...@tu-braunschweig.de
To: gmx-us...@gromacs.org
Subject: [gmx-users] Coulomb barriers and Coulomb Softcore Potential
Message-ID: 55db225c.8030...@tu-braunschweig.de
Content-Type: text/plain; charset=utf-8; format=flowed

Dear Gromacs-Users,

I want to calculate the solvation free energy of water in an aqueous
ionic solution and I'm using the Python tool alchemical-analysis.py by
Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a
very high N/N_k ratio (up to 7000) while decreasing the electrostatic
potential (Lennard Jones fully active).

Considering energetic barriers, I would like to adjust the Coulomb
Softcore Potential. Does this seem plausible and if so, how is the
Coulomb Softcore Potential defined in Gromacs?
Naden and Shirts provide a concept by equation (A.2) in Linear Basis
Function Approach to Efficient Alchemical Free Energy Calculations. 2.
Inserting and Deleting Particles with Coulombic Interactions
(http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula
intended?

Best regards,
Andreas



--
Yasser Almeida Hernández
PhD student
Institute

[gmx-users] Membrane protein insertion

[Yasser Almeida Hernández]

Hi all,

I want to insert a membrane protein into a model bilayer and I've tried 
several methods. The more straightforward seems to be Memembed, which 
gives an orientation to the membrane. On the other hand this method only 
outputs the membrane as dummy balls. How to translate this orientation 
to a model bilayer (DOPC, POPC)?


On the other hand I've tried InflateGRO2 for this purpose and I got this 
error (following the tutorial in 
https://code.google.com/p/inflategro2/wiki/TutorialTolC ):


Back Off! I just backed up ../1-topology/4hzuS_popc.top to 
../1-topology/#4hzuS_popc.top.3#
Will use a deflating factor of 0.925539817285086 to shrink the lipids 
back in 20 steps

Deflating
grompp -f deflate.mdp -c inflated.gro -p ../1-topology/4hzuS_popc.top -n 
inflated.ndx -o tmp.tpr -maxwarn 1

mdrun -s tmp.tpr -v -deffnm tmp_out -c shrink.00.gro
  -
ERROR: Cannot open GRO file shrink.00.gro: No such file or directory


The end of the log.out file is this:

Fatal error:
Too many LINCS warnings (1184)
If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file or set the environment variable 
GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem


Any thoughts?

Thanks in advance

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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Re: [gmx-users] Membrane protein insertion/orientation methods

[Yasser Almeida Hernández]

Thanks!

I ran LAMBADA and InflateGRO before to embed my protein in a POPC 
membrane, following the tutorial in 
https://code.google.com/p/inflategro2/wiki/TutorialTolC. It is possible 
that my protein is inserted tilted in the membrane.
When program ask for inflating group I choosed 13 (for POPC) and 1 for 
protein. When I run InflateGRO I got this error:


 Back Off! I just backed up ../1-topology/4hzuS_popc.top to 
../1-topology/#4hzuS_popc.top.3#
 Will use a deflating factor of 0.925539817285086 to shrink the lipids 
back in 20 steps

 Deflating
 grompp -f deflate.mdp -c inflated.gro -p ../1-topology/4hzuS_popc.top 
-n inflated.ndx -o tmp.tpr -maxwarn 1

 mdrun -s tmp.tpr -v -deffnm tmp_out -c shrink.00.gro
   -
 ERROR: Cannot open GRO file shrink.00.gro: No such file or directory

The end of the log.out file is this:

 Fatal error:
 Too many LINCS warnings (1184)
 If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file or set the environment variable

GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem

I checked for errors about this and it seems tha the system is blowing up...

Any thoughts?

Yasser

Am 21.08.2015 um 12:00 schrieb 
gromacs.org_gmx-users-requ...@maillist.sys.kth.se:

Date: Fri, 21 Aug 2015 10:31:58 +0100
From: Catarina A. Carvalheda dos Santos
c.a.c.dossan...@dundee.ac.uk
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: Re: [gmx-users] Membrane protein insertion/orientation
methods
Message-ID:
cago0fv_f342oxfcqtgrwn4s72bxhe+pa0e+kz4-uzgw9mou...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8

Hi there,

Lambada + InflateGRO2 is a good combination.

As for which method is the best one is difficult to say. If you read the
articles you will have a nice idea of the pros and cons of each method and
then you can decide by yourself. The only thing I can say is that after
reading them all I went for the aforementioned combination ;)

Cheers,
On 21 Aug 2015 10:08, Tsjerk Wassenaar tsje...@gmail.com wrote:


Hi Yasser,

InflateGRO and g_membed do not predict the insertion or orientation, but
require the protein to be oriented already. With InflateGRO2, Christian
Kandt also brought out LAMBADA which may help aligning a protein with the
membrane. memembed is also an orientation predictor. However, I usually
just get the protein from the orientations of proteins in membranes (OPM)
database at http://opm.phar.umich.edu/

Cheers,

Tsjerk

On Fri, Aug 21, 2015 at 10:16 AM, Yasser Almeida Hern?ndez 
yasser.almeida.hernan...@chemie.uni-hamburg.de wrote:


Hi all,

Among the methods available, which one is the best/more rigorous/popular
for membrane protein insertion/orientation in model bilayers (InflateGRO,
Memembed, g_membed, etc.)?

Thanks in advance

Yasser

--
Yasser Almeida Hern?ndez
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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--
Tsjerk A. Wassenaar, Ph.D.
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--



--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Membrane protein insertion/orientation methods

[Yasser Almeida Hernández]

Hi all,

Among the methods available, which one is the best/more rigorous/popular 
for membrane protein insertion/orientation in model bilayers 
(InflateGRO, Memembed, g_membed, etc.)?


Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] Gromacs 5.0.5 compilation error

[Yasser Almeida Hernández]

Hi all,

I am compiling Gromacs 5.0.5 and got this error:

../../lib/libgromacs_mpi.so.0.0.0: undefined reference to `__cudaInitModule'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

I installed the last version of CUDA toolkit libraries.

Thank in advance for your help.

Yasser

--
Yasser Almeida Hernández
PhD student
Department of Chemistry
Institute of Biochemistry and Molecular Biology
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
office: Grindelallee 117, room 250c



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