[gmx-users] Conserved quantity in NPT simulations
Hi, I am wondering how to test the conserved quantity in an NPT simulation fron the ener.edr file. As you well know for npt with a Nose-Hoover thermostat and a Parrinello-Rahman barostat, the conserved quantity is not just K+P, but contains additional terms function of the additional npt variables. Are those energies placed somewhere? I am using a somewhat new potential for a system and I want to know how well it conserves the energy at constant pressure and temperature. Thnaks in advance! Paolo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] installing on macbook
hi.. i have problem in installing gromacs in my macbook pro ( personal pc) .. can anyone help me with this?? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] installing on macbook
On 10/24/14 6:32 AM, Suraya Abdul Sani wrote: hi.. i have problem in installing gromacs in my macbook pro ( personal pc) .. can anyone help me with this?? Not unless you tell us exactly what you're doing - exact cmake command, exact error messages, etc. In general, follow http://www.gromacs.org/Documentation/Installation_Instructions -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conserved quantity in NPT simulations
Those conserved quantities are indeed included in the reported information. For thermostats/barostats where there is such a quantity, it's included in the .edr file. On Fri, Oct 24, 2014 at 4:23 AM, Paolo Franz paolo.fr...@gmail.com wrote: Hi, I am wondering how to test the conserved quantity in an NPT simulation fron the ener.edr file. As you well know for npt with a Nose-Hoover thermostat and a Parrinello-Rahman barostat, the conserved quantity is not just K+P, but contains additional terms function of the additional npt variables. Are those energies placed somewhere? I am using a somewhat new potential for a system and I want to know how well it conserves the energy at constant pressure and temperature. Thnaks in advance! Paolo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] installing on macbook
Hi Suraya. I have succesfully installed Gromacs 4.5, 4.6, and 5.0 on my macbook pro running OS X Mavericks, even with CUDA support. I am not using apple compiler because apple compiler in Mavericks (clang 3.4) doesn't support OpenMP, that will cause many errors when compiling gromacs (my experience) so that i use gcc 4.7 compiler instead. Here my step to install Gromacs on My MacbookPro mid 2009. FIRST: -Install GCC/G++ 4.7. Its very easy to install gcc/g++ 4.7 via MacPorts ( www.macports.org) because it is almost automatic as all dependencies will be installed. SECOND: -Download Gromacs 5.0/5.0.01/5.0.2 -Extract the downloaded file -open the downloaded folder in terminal. If you don't familiar how to open folder in terminal, then just right click - service -- new terminal at folder (if this options doesn't exists, do the following steps : system preferences -- keyboard -- shortcut -- service -- new folder at terminal) - just type: *cmake .. -DCMAKE_C_COMPILER=/opt/local/bin/gcc -DCMAKE_CXX_COMPILER=/opt/local/bin/g++ -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_BUILD_OWN_FFTW=ON *then press return/enter. - everything should be set up, and the fftw is also automatically downloaded and compiled. - then type *make -j 2 *(if your macbook has 2 cores) - then * make install* - run *make check *if you compile 5.0.2 - then type *export PATH=$PATH:/usr/local/gromacs/bin/* every time you want to start gromacs that's it. good luck On Fri, Oct 24, 2014 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 6:32 AM, Suraya Abdul Sani wrote: hi.. i have problem in installing gromacs in my macbook pro ( personal pc) .. can anyone help me with this?? Not unless you tell us exactly what you're doing - exact cmake command, exact error messages, etc. In general, follow http://www.gromacs.org/Documentation/Installation_ Instructions -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in the middle of running mdrun_mpi
Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1 fourierspacing = 0.12 fourier-nx= 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = Nose-Hoover tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = parrinello-rahman pcoupltype = Isotropic tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 refcoord-scaling = No gen-vel = no gen-temp = 298.00 gen-seed = -1 constraints = all-bonds constraint-algorithm = Lincs continuation = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for MD* integrator = md tinit = 0 dt = 0.001 nsteps = 5 ; 1 us init-step = 0 simulation-part= 1 comm-mode = Angular nstcomm = 100 comm-grps = system bd-fric = 0 ld-seed = -1 nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstcalcenergy = 1 nstenergy = 1 nstxtcout = 0 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 10 ns-type = simple pbc = no rlist= 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw = 0.5 DispCorr = No table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA ;implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80
Re: [gmx-users] error in the middle of running mdrun_mpi
On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1 fourierspacing = 0.12 fourier-nx= 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = Nose-Hoover tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = parrinello-rahman pcoupltype = Isotropic tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 refcoord-scaling = No gen-vel = no gen-temp = 298.00 gen-seed = -1 constraints = all-bonds constraint-algorithm = Lincs continuation = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for MD* integrator = md tinit = 0 dt = 0.001 nsteps = 5 ; 1 us init-step = 0 simulation-part= 1 comm-mode = Angular nstcomm = 100 comm-grps = system bd-fric = 0 ld-seed = -1 nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstcalcenergy = 1 nstenergy = 1 nstxtcout = 0 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 10 ns-type = simple pbc = no rlist= 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw = 0.5 DispCorr = No table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA ;implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1
[gmx-users] use of Walls in Martini simulations
Hi, I would like to post a question about simulating with Walls in gromacs and using the Martini force field. The question is very simple. I am trying to simulate a simple box of water molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen T-coupling and no pressure bath. I am trying: pbc=xy nwall =2 wall_atomtype = C1 C1 (C1 are the alkane carbons defined in the martini force field file) wall_type = 9-3 wall_density = 110 110 wall_r_linpot = 1 and all what I have is that the initial box of water molecules breaks in two pieces that separate each other in the z-direction. The same result (or a segmentation fault) is obtained by using 10-4 o 12-6 LJ potentials, large wall_r_linpot values, other values of wall_densities, so I think that the problem is with the wall_atomtype. I tried the water bead (W) instead, and segmentation fault is obtained. thank you very much in advance, Ramon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] numerical matrix from xpm file
Hi Tsjerk,
This is a very useful script. Just found a small bug that is only
noticeable if one is using higher -nlevels for the .xpm construction (in
g_rms, for example)
z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
should be
z = [colors[j[k:k+nb]] for k in range(0,nx*nb,nb)]
instead. At least that's working for me.
Thank you for sharing,
João
On Mon, Oct 4, 2010 at 12:05 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Anupam,
I recently wrote a small python script to convert gromacs .xpm files
to numbers. Maybe it'll be of some use to you:
Cheers,
Tsjerk
###
#!/usr/bin/env python
import sys
def unquote(s):
return s[1+s.find(''):s.rfind('')]
def uncomment(s):
return s[2+s.find('/*'):s.rfind('*/')]
def col(c):
color = c.split('/*')
value = unquote(color[1])
color = unquote(color[0]).split()
sys.stderr.write(%s: %s %s %s\n%(c.strip(),color[0], color[1],
value))
return color[0], value
# Open the xpm file for reading
xpm = open(sys.argv[1])
# Read in lines until we fidn the start of the array
meta = [xpm.readline()]
while not meta[-1].startswith(static char *gromacs_xpm[]):
meta.append(xpm.readline())
# The next line will contain the dimensions of the array
dim = xpm.readline()
# There are four integers surrounded by quotes
nx, ny, nc, nb = [int(i) for i in unquote(dim).split()]
# The next dim[2] lines contain the color definitions
# Each pixel is encoded by dim[3] bytes, and a comment
# at the end of the line contains the corresponding value
colors = dict([col(xpm.readline()) for i in range(nc)])
for i in xpm:
if i.startswith(/*):
continue
j = unquote(i)
z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
sys.stdout.write( .join(z)+\n)
###
On Mon, Oct 4, 2010 at 12:33 PM, Anupam Nath Jha
anu...@mbu.iisc.ernet.in wrote:
right. I also came to see one of them but with no result.
and since it was done some time back so I thought if some one has come
up with
some method to get that.
right now I wanted the matrix information obtained from command
g_mdmat.
can you suggest some way to get that.
thanks
anupam
No, there's no ability to do this. I think there should be, though, and
seem to
recall discussion of it on one or other mailing list or the web page.
Mark
- Original Message -
From: Anupam Nath Jha anu...@mbu.iisc.ernet.in
Date: Saturday, October 2, 2010 21:32
Subject: [gmx-users] numerical matrix from xpm file
To: gmx-us...@gromacs.org
Hi all
Is it possible to obtain the matrix in numeric form from xpm
(obtained from
gromacs analysis) files.
because it's not coming in options for ourput files.
thanks with regards
anupam
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--
Science is facts; just as houses are made of stone, so is science is
made of
facts; but a pile of stones is not a house, and a collection of facts
is not
necessarily science.
Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] use of Walls in Martini simulations
What about electrostatics? Ewald summation is probably the culprit here. On Oct 24, 2014 12:05 PM, Ramon Reigada reig...@ub.edu wrote: Hi, I would like to post a question about simulating with Walls in gromacs and using the Martini force field. The question is very simple. I am trying to simulate a simple box of water molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen T-coupling and no pressure bath. I am trying: pbc=xy nwall =2 wall_atomtype = C1 C1 (C1 are the alkane carbons defined in the martini force field file) wall_type = 9-3 wall_density = 110 110 wall_r_linpot = 1 and all what I have is that the initial box of water molecules breaks in two pieces that separate each other in the z-direction. The same result (or a segmentation fault) is obtained by using 10-4 o 12-6 LJ potentials, large wall_r_linpot values, other values of wall_densities, so I think that the problem is with the wall_atomtype. I tried the water bead (W) instead, and segmentation fault is obtained. thank you very much in advance, Ramon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Multiple writing to same trajectory issue
Just one more question on that topic: according to the Hoempage (http://www.gromacs.org/Documentation/How-tos/Doing_Restarts - After a crash), it used to be possible to resume a crashed run by employing tpbconv and supplying the trr file. As I did not save my cpt-files, would that still be an option (I saved frames to trr every now and then...)? If so, I could at least save a big part of my data and recover the broken run somewhere before the point of the crash. If I understand it correctly, this would give me a continous trajectory even though I think I will have to manually join the data. Is this correct? Thank you for your help, Matthias On 10/16/2014 05:38 PM, Mark Abraham wrote: Only if there is still a matching checkpoint file from that time, which would only be true if the resumed runs didn't proceed very far, or you kept a backup somehow. Mark -- Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Question about Walls
Hi, I would like to post a question about simulating with Walls in gromacs. The question is very simple. I am trying to simulate a simple box of water molecules with pbc=xy and walls at z=0 and z=z_box. I use Berendsen T-coupling and no pressure bath. I am trying: pbc=xy nwall =2 wall_atomtype = C1 C1 (C1 are the alkane carbons defined in the martini force field file) wall_type = 9-3 wall_density = 110 110 wall_r_linpot = 1 and all what I have is that the initial box of water molecules breaks in two pieces that separate each other in the z-direction. The same result (or a segmentation fault) is obtained by using 10-4 o 12-6 LJ potentials, large wall_r_linpot values, other values of wall_densities, so I think that the problem is with the wall_atomtype. I tried the water bead (W) instead, and segmentation fault is obtained. thank you very much in advance, Ramon Aquest correu electrònic i els annexos poden contenir informació confidencial o protegida legalment i està adreçat exclusivament a la persona o entitat destinatària. Si no sou el destinatari final o la persona encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu rebut aquest correu electrònic per error, us preguem que n’informeu al remitent i que elimineu del sistema el missatge i el material annex que pugui contenir. Gràcies per la vostra col·laboració. Este correo electrónico y sus anexos pueden contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no es el destinatario final o la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha recibido este mensaje electrónico por error, le rogamos que informe al remitente y elimine del sistema el mensaje y el material anexo que pueda contener. Gracias por su colaboración. This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cannot combine residue position based cog selection with index output for g_select
Hi, I have a system consists of a box of water and a monolayer of polymer in the center. I am trying to extract solvent molecules that have z coordinates greater than 5 nm using g_select and output an index file. Basically I want to separate my system into two portions: a box of waters above the monolayer and the rest of the system containing the monolayer. With the water only portion extracted by trajconv, I want to use genion to replace some water molecules with salt and put this modified portion back to my system that contains the monolayer. Right now, I am able to use g_select -on -select resname SOL and z5 to select all atoms that belong to SOL and has z 5 nm. However, this way does not guarantee that all the atoms selected are from SOL molecules whose cog are above z=5 plane. And as a result, some atoms that are part of SOL molecules below the z=5 plane are also selected and the entire selection contains some complete water molecules and some atoms that are from below plane water molecules (incomplete waters). I am not sure with this kind of selection, if I extract it with trajconv, and replace water with salt by genion, and then put it back to original system, will I get correct alignment of those atoms from incomplete water molecules and get the desired configuration. ( I think genion will only replace complete residue; however, when using trajconv to generate new coordination files, I am not sure if the system will be re-set to origin or not. If so then the coordinates will definitely be misplaced and when I put the modified part back there will be misalignment). TO AVOID all that, I'd like to use cog of SELECTION option in the g_select, except for 1 problems: the -on option only works with atom selection. So my essential question is: is there a way to use g_select with both the -on option and cog option? Or is there another way to finish my task? I have searched the archive and did not find something that answers my question. Thank you all for helping out. Best, Dongxu Huang Graduate student at Northwestern University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
