[gmx-users] how to do dPCA?

[Seera Suryanarayana]

Dear gromacs users

I would like to do dPCA for my 100ns trajectory. When see in the gromacs
tutorial I could not create the covar.ndx file. My peptide is 20 residues
length. I made .ndx file for dihedral angles and after generating the
dangle.trr file. But here I have one problem, to generate the .gro file we
have to create the covar.ndx file based on the 2*N/3 formula. As my peptide
has 20 dihedral angles, the covar.ndx file will have 14 atoms. But I want
to generate .gro file to my complete peptide (20 residues). I request you
to here help me out.

Thanks in advance
Surya
Graduate student
India.
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Re: [gmx-users] grompp error

[Dallas Warren]

My guess would be that when you thought ran it with the increased box
size coordinate file, you actually used the original coordinate file.

FYI 
http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 16 October 2017 at 12:22, Amali Guruge  wrote:
> Dear Gromacs users,
>
> I got the following error when I tried to run grompp.
> ERROR 1 [file system.top, line 18]:
>   ERROR: One of the box lengths is smaller than twice the cut-off length.
>   Increase the box size or decrease rlist
>
> I increased the box size and re-tried to run grompp,but it didn't work. The
> box size is 20*20*20 nm3. mdp file options are shown in below. Could you
> please anyone help me to solve this problem.
>
> Thank you.
>
> ; Define can be used to control processes
> define  = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator= steep; Algorithm (steep = steepest descent
> minimization)
> emtol= 1.0; Stop minimization when the maximum force < 1.0
> kJ/mol
> nsteps= 200; Maximum number of (minimization) steps to
> perform
> nstenergy= 10; Write energies to disk every nstenergy steps
> nstcalcenergy= 10; Calculate energy every step
> energygrps= System; Which energy group(s) to write to disk
> nstxout   = 100  ; Frequency of writing to .trr file
>
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> cutoff-scheme   = Verlet
> ns_type= simple; Method to determine neighbor list (simple,
> grid)
> coulombtype= cut-off; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0; long range electrostatic cut-off
> rvdw= 1.0; long range Van der Waals cut-off
> constraints= none; Bond types to replace by constraints
> pbc= xyz; Periodic Boundary Conditions (yes/no)
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Re: [gmx-users] gromacs error

[Justin Lemkul]

On 10/16/17 12:17 PM, Rahma Dahmani wrote:

Hi,
How can i rectify the following GROMACS error?
Fatal error:
atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms
while sorting atoms.


Either correct the atom names to what the force field expects, or 
simplify life and use -ignh to have pdb2gmx rebuild the H atoms.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] gromacs error

[Rahma Dahmani]

Hi,
How can i rectify the following GROMACS error?
Fatal error:
atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms
while sorting atoms.

Thank you for your help
-- 






*Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
Tunisie Tél: (+216) 28151042*
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Re: [gmx-users] new i9 processor

[Szilárd Páll]

On Mon, Oct 16, 2017 at 2:56 PM, Harry Mark Greenblatt
 wrote:
> BS”D
>
> Dear Bernard,
>
>   Thank you for your reply and info.  Our experience with a second graphics 
> card (when coupled with the appropriate number of cores) is that we garner 
> close to a 100% performance gain.  We have access to nodes on a cluster with 
> 16 cores (2 x E5-2630 v3) + 1 K80 (dual gpu on each card).   If I recall 
> correctly, in our initial tests of those nodes, we compared 8 cores + 1 gpu 
> vs 16 cores + 2gpu’s, and got close to double the performance.  This is also 
> consistent with our performance on our workstations, most of which have a 
> hexacore Xeon coupled to a Geforce GTX 770 (or 970 in more recent versions).  
> Use of the 16 cores + dual GPU compute nodes gives us close to double the 
> performance relative to the workstations.  I suspect that your dual K40’s are 
> only showing a 5-10% gain over the single Geforce card because the GTX 1080i 
> on your workstations should be significantly faster than the K40 on the 
> nodes.  This is due to the newer architecture (Pascal vs. Kepler), higher 
> core count (3584 vs. 2880), and the higher clock speeds (1480 base vs. 745 
> base) on the 1080ti.
>
> I recall a statement by Szilárd once, in some email, about getting very good 
> scaling (i.e., close to linear) with multiple GPU’s.

I hope I did say exactly that because in general it is not true: both
because we're accelerating (for now) a single task and because offload
to multiple GPU requires domain-decomposition.
The switch from no DD (only multi-threading) to DD has an initial hit
and going from 1 to 2 GPU you can therefore often see fairly moderate
scaling. From e.g. 2 to 4-way DD you can get near-linear scaling, but
it will depend on the system size.

Scaling to multiple GPUs, especially if by that you mean using the
same number of cores and increasing the GPU count will certainly not
give linear scaling in performance (time-to-solution) as only part of
the computation is reduced -- if that scales at all.

So generally: you'll need a well-balanced CPU cores to GPU ratio and
increasing the GPUs count only will only help if the run in GPU-bound
(and even than, only by a limited amount).

We're hoping to get some new features in the development branch soon
which will change some of these assumptions!

Cheers,
--
Szilárd

> Thanks again,
>
>
> Harry
>
>
> Dear Harry,
>
> we have several nodes with single i9 7900 decacore processors and one gtx 
> 1080ti each. So far they show very good performance compared with dual 16 
> core xeon nodes with two K20x and even K40x cards. We reach a performance of 
> >40ns per day for >9 atoms with the i9 system, compared to 50 ns/day with 
> the dual xeon + dual K40x and 30 ns/day with the dual xeon + dual K20x. So 
> your configuration should easily outrun the xeon setups... since you want to 
> use the 16 core i9 the second gtx you propose might even make sense but mb 
> you should reconsider if the 5-10% speedup with the second card is really 
> worth the buck ...
>
> Best,
>
>
>
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology   
> harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
> Weizmann Institute of SciencePhone:  972-8-934-6340
> 234 Herzl St.Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
>
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Re: [gmx-users] Question about "gmx traj" command

[Justin Lemkul]

On 10/16/17 9:36 AM, Chang Woon Jang wrote:

Dear Gromacs Users,

 I have a question about the gmx traj in order to calculate the force
components.

I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr
-af force_all_z_l9.xvg -z yes

It produced "force_all_z_l9.xvg" file. In the file, there are four columns.
The first column should be the atom ID.

My question is what is the rest of columns? For example, some of the values
are negative and the other values are positive.

-z yes means the plot of Z-component in the manual. I do not know what the
exact meaning of three columns. Would you please give me a comment on that?


You're getting (x,y,z) because you haven't turned them off (note from 
the help info that all dimensions are on by default).


All you need is:

gmx traj ... -nox -noy -z

-Justin


Thank you.


# This file was created Mon Oct 16 21:53:33 2017
# Created by:
#:-) GROMACS - gmx traj, 2016.4-dev-20170620-8d2584c-unknown (-:
#
# Executable:  /home/chang/Packages/votca/bin/gmx
# Data prefix:  /home/chang/Packages/votca
# Working dir:  /home/chang/2017_NU_PROJECT/1_FIRST_PROJECT/1_Less_5Million/
5_REVERSED_ATOMISTIC_TEST/1_Lambda_9/1_TENSION/1_SR10e8_l9_
300K/ANALYSIS/7_Force_Component
# Command line:
#  gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z yes
# gmx traj is part of G R O M A C S:
#
# Gromacs Runs One Microsecond At Cannonball Speeds
#
@title "average force"
@xaxis  label "Atom"
@yaxis  label "Spatial component"
@TYPE xy
1-11.866  42.002  29.565
2  22.660-11.028-21.749
3  -0.232  -3.681  4.181
4  -9.308-31.931-22.545
5-27.221-21.572  7.099
6  11.648  4.523  -8.757
7  32.491  0.888  17.891


Best regards,
Changwoon Jang


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Question about "gmx traj" command

[Chang Woon Jang]

Dear Gromacs Users,

I have a question about the gmx traj in order to calculate the force
components.

I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr
-af force_all_z_l9.xvg -z yes

It produced "force_all_z_l9.xvg" file. In the file, there are four columns.
The first column should be the atom ID.

My question is what is the rest of columns? For example, some of the values
are negative and the other values are positive.

-z yes means the plot of Z-component in the manual. I do not know what the
exact meaning of three columns. Would you please give me a comment on that?

Thank you.


# This file was created Mon Oct 16 21:53:33 2017
# Created by:
#:-) GROMACS - gmx traj, 2016.4-dev-20170620-8d2584c-unknown (-:
#
# Executable:  /home/chang/Packages/votca/bin/gmx
# Data prefix:  /home/chang/Packages/votca
# Working dir:  /home/chang/2017_NU_PROJECT/1_FIRST_PROJECT/1_Less_5Million/
5_REVERSED_ATOMISTIC_TEST/1_Lambda_9/1_TENSION/1_SR10e8_l9_
300K/ANALYSIS/7_Force_Component
# Command line:
#  gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z yes
# gmx traj is part of G R O M A C S:
#
# Gromacs Runs One Microsecond At Cannonball Speeds
#
@title "average force"
@xaxis  label "Atom"
@yaxis  label "Spatial component"
@TYPE xy
1-11.866  42.002  29.565
2  22.660-11.028-21.749
3  -0.232  -3.681  4.181
4  -9.308-31.931-22.545
5-27.221-21.572  7.099
6  11.648  4.523  -8.757
7  32.491  0.888  17.891


Best regards,
Changwoon Jang
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Re: [gmx-users] new i9 processor

[Bernhard Reuter]

Dear Harry,

you are right for the dual xeon 16 core setup you (and we) use, but for 
the single core i9 setup we made the experience, that we only gained 
between 5-10% of performance by adding a second gpu. This was what I was 
hinting here...


Best Bernhard


Am 16/10/17 um 14:56 schrieb Harry Mark Greenblatt:

BS”D

Dear Bernard,

   Thank you for your reply and info.  Our experience with a second graphics 
card (when coupled with the appropriate number of cores) is that we garner 
close to a 100% performance gain.  We have access to nodes on a cluster with 16 
cores (2 x E5-2630 v3) + 1 K80 (dual gpu on each card).   If I recall 
correctly, in our initial tests of those nodes, we compared 8 cores + 1 gpu vs 
16 cores + 2gpu’s, and got close to double the performance.  This is also 
consistent with our performance on our workstations, most of which have a 
hexacore Xeon coupled to a Geforce GTX 770 (or 970 in more recent versions).  
Use of the 16 cores + dual GPU compute nodes gives us close to double the 
performance relative to the workstations.  I suspect that your dual K40’s are 
only showing a 5-10% gain over the single Geforce card because the GTX 1080i on 
your workstations should be significantly faster than the K40 on the nodes.  
This is due to the newer architecture (Pascal vs. Kepler), higher core count 
(3584 vs. 2880), and the higher clock speeds (1480 base vs. 745 base) on the 
1080ti.

I recall a statement by Szilárd once, in some email, about getting very good 
scaling (i.e., close to linear) with multiple GPU’s.

Thanks again,


Harry


Dear Harry,

we have several nodes with single i9 7900 decacore processors and one gtx 1080ti 
each. So far they show very good performance compared with dual 16 core xeon nodes 
with two K20x and even K40x cards. We reach a performance of >40ns per day for 
>9 atoms with the i9 system, compared to 50 ns/day with the dual xeon + dual 
K40x and 30 ns/day with the dual xeon + dual K20x. So your configuration should 
easily outrun the xeon setups... since you want to use the 16 core i9 the second gtx 
you propose might even make sense but mb you should reconsider if the 5-10% speedup 
with the second card is really worth the buck ...

Best,




Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel



--
Dipl.-Phys. Bernhard Reuter
Theoretical Biophysics Subgroup
Theoretical Physics II
Institute of Physics
University of Kassel
Heinrich-Plett-Str. 40
34132 Kassel, Germany
Tel: +49 561 804 4482
Mobile: +40 152 27331699
https://www.researchgate.net/profile/Bernhard_Reuter


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[gmx-users] possible bug in convert-tpr

[Albert Solernou]

Hi All,
I think that there is a bug in "gmx convert-tpr", as I understand that 
"gmx dump" dumps wrong atom types and some wrong numbers when working 
with some modified tpr files. I attach clear instructions on how to get 
the bug, as well as two input files and the faulty .trp.


I found the problem using VOTCA's command csg_dump, and reported it to them:
   https://groups.google.com/forum/#!topic/votca/ogRTNFRL4RA
but after some discussion they said I should report it to you.

Could you please have a look at this? Please have a read at the 
discussion in VOTCA's email list to make sense of it all.


Many thanks,
Albert

P. S. - I just attached the most basic files to reproduce the bug. I 
could attach more, but that would exceed the 50K limit that the list 
imposes. In any case, the rest of the files can be found in the VOTCA 
email thread, previously commented.




--
-
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

A 32 GLN
A 35 VAL
A 36 VAL
A 37 PHE
A 38 GLN
A 39 ASN
A 40 ARG
A 41 GLU
A 43 VAL
A 54 GLU
A 64 THR
A 65 ARG
A 66 GLY
A 67 THR
A 69 ARG
A 84 ASP
A 85 HIS
A 86 TYR
A 87 ALA
B 17 HIS
B 29 TYR
B 30 TYR
B 31 GLY
B 33 ASN
B 34 LEU
B 35 ASP
B 36 ALA
B 38 TRP
B 39 ASP
B 40 CYS
B 42 THR
B 43 GLY
B 44 TRP
B 73 VAL
B 76 GLU
[ Interface ]
 432  433  434  435  436  437  438  439  440  441  442  443  444  445  446 
 447  448  468  469  470  471  472  473  474  475  476  477  478  479  480 
 481  482  483  484  485  486  487  488  489  490  491  492  493  494  495 
 496  497  498  499  500  501  502  503  504  505  506  507  508  509  510 
 511  512  513  514  515  516  517  518  519  520  521  522  523  524  525 
 526  527  528  529  530  531  532  533  534  535  536  537  538  539  540 
 541  542  543  544  545  546  547  548  549  550  551  552  553  554  555 
 556  557  558  559  560  561  562  563  564  565  566  567  568  569  570 
 571  572  573  574  575  576  577  578  579  580  581  582  583  584  585 
 586  587  588  589  601  602  603  604  605  606  607  608  609  610  611 
 612  613  614  615  616  779  780  781  782  783  784  785  786  787  788 
 789  790  791  792  793  933  934  935  936  937  938  939  940  941  942 
 943  944  945  946  947  948  949  950  951  952  953  954  955  956  957 
 958  959  960  961  962  963  964  965  966  967  968  969  970  971  972 
 973  974  975  976  977  978  979  980  981  982  983  984  985  986  987 
 988  989  990  991 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 
1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1245 1246 
1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 
1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 
1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 
1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1701 1702 
1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 
1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 
1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 
1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 
1949 1950 1951 1952 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 
1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 
1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 
2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2042 
2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 
2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 
2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 
2088 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 
2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 
2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 
2152 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 
2626 2627 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 
2685 2686 
# Gromacs - parse the PDB, define a box, solvate, neutralise with ions and 
minimise:
gmx pdb2gmx -f 1ay7.pdb -merge all -ignh -o gmx1ay7.pdb
gmx editconf -f gmx1ay7.pdb -o 1ay7.gro -d 1.0 -bt dodecahedron
gmx solvate -cp 1ay7.gro -cs spc216.gro -o 1ay7Solv.gro -p topol.top
gmx grompp -f ions.mdp -c 1ay7Solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o 1ay7SolvIons.gro -p topol.top -pname NA -nname CL -np 
13
gmx grompp -f minim-slow.mdp -c 1ay7SolvIons.gro -p topol.top -o em.tpr
mpirun  gmx_mpi mdrun -v -pin on -deffnm em

# Gromacs - start equilibration: a short trajectory at 100K, NVT:
gmx grompp -f nvt-100.mdp -c em.gro -p topol.top  -o nvt-100.tpr
mpirun  gmx_mpi mdrun -v -pin on -deffnm nvt-100

# interfaceResidues.txt is a list of residues at the interface of 

[gmx-users] Fw: Two questions about PME-User in coulombtype

[Du, Yu]

Dear Hess, 

I have two questions about the usage of the PME-User in coulombtype parameter.
I didn't get replies from the GMX-USER mail list. Could you please give some 
details? The forwarded mail is the two questions I asked.

Thanks for your help.

Yu

-Original Messages-
From: "Du, Yu" 
Sent Time: 2017-10-15 17:17:14 (Sunday)
To: GMX-user 
Subject: [gmx-users] Two questions about PME-User in coulombtype

Hi GMX Users, 


I'm using tabulized potentials between energygrp-table = Protein Ligand. I'm 
writing to inquiring the details of PME-User parameter.


I have seen some discussions in the GMX User mail list and the explanation in 
user guide. I still can't ensure I have grasped the meaning of PME-User in 
coulombtype option. The following is my understanding. If anything is wrong 
please point out. Thanks a lot.


1) Because the mesh part also contributes below the cut-off, the PME mesh 
contribution is subtracted from the user table by gmx mdrun to get the 
short-range coulombic interaction below the rcoulomb.


2) The tabulized potential is short-range interaction. If I use 
coulombtype=User, I only have the short-range interaction defined in the 
tabulized potetial files and no PME between any components (i.e. Protein, 
Ligand, SOL, ions) in the system.


3)If I use coulombtype=PME-User instead, I will get the short-range interaction 
defined in the tabulized potetial files and PME between any components (i.e. 
Protein, Ligand, SOL, ions) in the system like normal coulombtype=PME.


--Next Question--
"The PME mesh contribution is subtracted from the user table by gmx mdrun. 
Because of this subtraction the user tables should contain about 10 decimal 
places."
The second question is how to deal with the PME-User's "10 decimal places" in 
user guide of the coulombtype option. Does it mean that the original step of r 
= 0.002 nm in mixed precision should be 0.0# nm? What should be the 
detailed step size of r?



--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

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Re: [gmx-users] Energy minimization issue

[Justin Lemkul]

On 10/16/17 5:19 AM, Khadija Amine wrote:

Dear Gromacs users,

I'm simulation a double chain protein-ligand complex using Amber force
field. I have written parameters and generated the topology.

The energy minimization of the complex gives me the following error:

*Energy minimization has stopped, but the forces have not converged to the*

*requested precision Fmax < 1000 (which may not be possible for your
system).*

*It stopped because the algorithm tried to make a new step whose size was
too*

*small, or there was no change in the energy since last step. Either way,
we*

*regard the minimization as converged to within the available machine*

*precision, given your starting configuration and EM parameters*

*Double precision normally gives you higher accuracy, but this is often not*

*needed for preparing to run molecular dynamics.*

*You might need to increase your constraint accuracy, or turn*

*off constraints altogether (set constraints = none in mdp file)*
Could you please tell me what is the issue and provide some suggestions


http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Water tracking along simulation

[Justin Lemkul]

On 10/16/17 7:16 AM, Yasser Almeida Hernández wrote:

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.




Contact the corresponding author and see how they did what they did.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Regarding Residue in chain has different type (Other) from starting residue

[Justin Lemkul]

On 10/15/17 11:27 PM, Dilip H N wrote:

Thank you Justin Sir,

1] But how do i solve this issue..?? and make sure that pdb2gmx is not
interpreting my input as being a single chain and it's finding dissimilar
residue types..?? even i tried with gmx pdb2gmx with -ter command, but
still, i am getting the same results


There's no indication of a problem. If your input PDB file doesn't have 
TER delimiters between chains, then pdb2gmx -ter will do nothing.



2] If i view the structure in VMD and type protein in Graphical
representations->selected atoms, I am viewing only Glycine, and if i type
resname TMAO then i am viewing the tmao molecules ..., any inference here
can i have here..??


No, because what you see in VMD has no bearing on what pdb2gmx 
interprets. But as far as I can see, there's no actual problem to solve 
here.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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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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Re: [gmx-users] new i9 processor

[Mark Abraham]

Hi,

There's no real issue there. If anything, it's simpler. With the dual
socket system it would often make no sense to extend an OpenMP region
across the sockets. That's still true if there's internal structure that
makes some cores further from others (I dunno if true for Skylake-X). You'd
still want to use GROMACS in the same general way.

A 14-core node would make more complex structure harder to set up and use,
because 7 is prime. For example, a multi-sim setup using two simulations
each of two ranks on such a node would not have a natural way to split over
four ranks.

Mark

On Mon, Oct 16, 2017 at 11:59 AM Harry Mark Greenblatt <
harry.greenbl...@weizmann.ac.il> wrote:

> BS”D
>
> Dear All,
>
>   The new Skylake-X CPU’s have very high core counts, and could, in
> theory, take the place of a two socket 16 core Xeon system.  One could
> create a machine as follows:
>
> 1 x Core i9 7960X with 16 cores
> 2 x Geforce 1080 graphic cards,
>
> and run a simulation with 2 MPI ranks, coupling 8 cores to 1 gpu per rank.
>
> Would there be any technical problems arising from the single socket
> configuration, as opposed to a dual socket Xeon setup?  Any issues if a 14
> core processor was used (7 cores per rank, i.e., an odd number)?
>
> Thanks
>
> Harry
>
>
>
>
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology   harry.greenbl...@weizmann.ac.il
> <../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%
> 40weizmann.ac.il>
> Weizmann Institute of SciencePhone:  972-8-934-6340
> 234 Herzl St.Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Walls and center of mass motion

[Anders Støttrup Larsen]

Any ideas?

Anders

On Fri, Oct 13, 2017 at 3:15 PM, Anders Støttrup Larsen  wrote:

> Hi all
>
> I have been trying to simulate a system containing two walls and a
> slab/vacuum. During the simulation water from the slab diffuses into the
> vacuum as intended. The problem is that this causes the slab to move in the
> z-direction and eventually crash into one of the walls. The slab has a
> thickness of 60 Å and there is approximately 220 Å of vacuum at both
> sides of the slab.
>
> When using *nwall=2 *GROMACS turns off center of mass motion removal in
> the z-direction, is there any way to turn this back on? Or some other
> solution that makes sure the slab doesn’t move?
>
> I have attached the relevant part of the mdp.
>
>
> comm-mode   = Linear
>
> pbc   = xy
>
> ewald-geometry  = 3dc
>
> nwall = 2
>
> wall-type= 12-6
>
> wall-r-linpot= -2
>
> wall-atomtype= c c
>
> wall-density   = 40 40
>
> wall-ewald-zfac  = 3
>
>
>
> Anders
>
>
> 
>  Virusfri.
> www.avast.com
> 
> <#m_5462244576341608737_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
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[gmx-users] new i9 processor

[Harry Mark Greenblatt]

BS”D

Dear All,

  The new Skylake-X CPU’s have very high core counts, and could, in theory, 
take the place of a two socket 16 core Xeon system.  One could create a machine 
as follows:

1 x Core i9 7960X with 16 cores
2 x Geforce 1080 graphic cards,

and run a simulation with 2 MPI ranks, coupling 8 cores to 1 gpu per rank.

Would there be any technical problems arising from the single socket 
configuration, as opposed to a dual socket Xeon setup?  Any issues if a 14 core 
processor was used (7 cores per rank, i.e., an odd number)?

Thanks

Harry





Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel

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[gmx-users] Energy minimization issue

[Khadija Amine]

Dear Gromacs users,

I'm simulation a double chain protein-ligand complex using Amber force
field. I have written parameters and generated the topology.

The energy minimization of the complex gives me the following error:

*Energy minimization has stopped, but the forces have not converged to the*

*requested precision Fmax < 1000 (which may not be possible for your
system).*

*It stopped because the algorithm tried to make a new step whose size was
too*

*small, or there was no change in the energy since last step. Either way,
we*

*regard the minimization as converged to within the available machine*

*precision, given your starting configuration and EM parameters*

*Double precision normally gives you higher accuracy, but this is often not*

*needed for preparing to run molecular dynamics.*

*You might need to increase your constraint accuracy, or turn*

*off constraints altogether (set constraints = none in mdp file)*
Could you please tell me what is the issue and provide some suggestions

Thank you
*Best regards*
*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
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