[gmx-users] Exploding box after 55.5ns of simulation
Dear GROMACS users,
I am running a NPT simulation of a 28 residue protein in a truncated
dodecahedron box of TIP4P water at 300K and 1bar. The force field is
OPLSAA 2001. The system ran fine for 55.5 ns and then it crashed due
to an exploding box. As the box was exploding, the potential energy
increased from -209 kJ to -204 kJ, the box volume went from 150 to
223, the pressure shot up to 897 bar from an average of 1bar, the
temperature increased from 300K to 317 K, and the total energy
increased from -171 kJ to -164 kJ.
>From reading the mailing archive, perhaps changing tau_p from 1.0 to
10.0 or 20.0 may solve the problem. Can anyone else please provide
suggestions? Others exploding box problems documented in the mailing
archive seem to occur early in the simulation and not after 55.5 ns.
It troubles me that the system ran fine for 55.5 ns before crashing.
Starting at time point 41.2 ns, "Correcting invalid box:" messages
start to appear but that's harmless according to various posting in
the mailing list.
This is how I generated my box:
editconf -f Pro8.gro -o Pro8.gro -d 1.2 -bt dodecahedron
genbox -cp Pro8.gro -cs tip4p.gro -o Pro8_b4em.gro -p Pro8.top
I am using gromacs 3.3.1 I have provided a snippet of the log that
warns of exploding box and my mdp file.
Correcting invalid box:
old box (3x3):
old box[0]={ 7.11699e+00, 0.0e+00, 0.0e+00}
old box[1]={ 0.0e+00, 7.11699e+00, 0.0e+00}
old box[2]={ 3.56227e+00, -3.55472e+00, 4.98818e+00}
new box (3x3):
new box[0]={ 7.11699e+00, 0.0e+00, 0.0e+00}
new box[1]={ 0.0e+00, 7.11699e+00, 0.0e+00}
new box[2]={-3.55472e+00, -3.55472e+00, 4.98818e+00}
Grid: 14 x 14 x 10 cells
WARNING: your box is exploding! (ncells = 1960)
Step Time Lambda
277555500.003910.0
Below is my mdp file
title = Pro
cpp = /lib/cpp
integrator = md
dt = 0.002
nsteps = 15000 ; 300ns
nstxout = 1
nstvout = 1
nstlog = 1
nstenergy = 1
nstxtcout = 1000
nstcomm = 1
comm_grps = Protein
xtc_grps= protein
energygrps = protein CL- SOL
ns_type = grid
coulombtype = pme
nstlist = 10
rlist = 1.0
rvdw= 1.0
optimize_fft= yes
tcoupl = berendsen
tc-grps = protein SOL CL-
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
Pcoupl = Parrinello-Rahman
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp= 300
gen_seed= -1
constraints = hbonds
Thank you,
JW
--
JW Feng
Ph.D. Candidate
Center for Computational Biology
Washington University in St. Louis
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Re: [gmx-users] t-couple warning
>From reading the wiki, it seems like it is better to couple the entire system to one thermostat. Would this better? tc_grps = system Thanks, JW On 10/11/07, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting JW Feng <[EMAIL PROTECTED]>: > > > Hello, > > > > This is a new warning that appears when executing version 3.3.2 of > > grompp to create a .tpr file. Should I be concerned? > > > > WARNING 1 [file aminoacids.dat, line 1]: > > T-Coupling group PROTEIN has fewer than 10% of the atoms (504 out of > > 24494) > > Maybe you want to try Protein and Non-Protein instead? > > WARNING 2 [file aminoacids.dat, line 1]: > > T-Coupling group CL- has fewer than 10% of the atoms (5 out of 24494) > > Maybe you want to try Protein and Non-Protein instead? > > > > My mdp options are: > > ;; TEMPERATURE COUPLING > > tcoupl = berendsen > > tc_grps = PROTEIN SOL CL- > > tau_t = 0.1 0.1 0.1 > > ref_t = 300 300 300 > > Don't couple solvent and ions separately. Merge them into one group with > make_ndx. > > http://wiki.gromacs.org/index.php/Thermostats > > -Justin > > > > > Thank you, > > > > JW > > > > -- > > Jianwen A Feng > > Center for Computational Biology > > Washington University in St. Louis > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > == > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > == > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] t-couple warning
Hello, This is a new warning that appears when executing version 3.3.2 of grompp to create a .tpr file. Should I be concerned? WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group PROTEIN has fewer than 10% of the atoms (504 out of 24494) Maybe you want to try Protein and Non-Protein instead? WARNING 2 [file aminoacids.dat, line 1]: T-Coupling group CL- has fewer than 10% of the atoms (5 out of 24494) Maybe you want to try Protein and Non-Protein instead? My mdp options are: ;; TEMPERATURE COUPLING tcoupl = berendsen tc_grps = PROTEIN SOL CL- tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 Thank you, JW -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem
Using "trjconv -ur compact -pbc atom" worked. JW On 10/9/07, JW Feng <[EMAIL PROTECTED]> wrote: > GMX users, > > In 3.3.1, I used "trjconv -ur compact -pbc whole " to convert a > rhombic dodecahedron box so it could be displayed properly in VMD. > This does not appear to be working in 3.3.2. Is there another way to > convert a box so it displays properly in a visualization program? > > This is the command that I used, > " echo 0 | trjconv -ur compact -pbc whole -f 1fsv_heat300.gro -s > 1fsv_heat300.gro -o 1fsv_heat300_visual.gro" > > Thanks, > > JW > > -- > Jianwen A Feng > Center for Computational Biology > Washington University in St. Louis > -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem
GMX users, In 3.3.1, I used "trjconv -ur compact -pbc whole " to convert a rhombic dodecahedron box so it could be displayed properly in VMD. This does not appear to be working in 3.3.2. Is there another way to convert a box so it displays properly in a visualization program? This is the command that I used, " echo 0 | trjconv -ur compact -pbc whole -f 1fsv_heat300.gro -s 1fsv_heat300.gro -o 1fsv_heat300_visual.gro" Thanks, JW -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] solubility of PVME in TIP5P
Did you noticed that the number of TIP5P water molecules is about half of what's needed to fill the box. I think that's why your box collapsed. JW On 4/23/07, kitty ji <[EMAIL PROTECTED]> wrote: > > > > > Dear GMX user, > > > > Explicated model of Poly (vinyl methyl ether) was built with ether > parameters in OPLS Force Field. The density and radius of gyration of PVME > melts fit experimental value well. And then it was solvated in Tip5p. > > > > In experiment, PVME should solvate in water well in ~300k. However, it > totally collapsed in my model. I have changed temperature and electricity > but no help. > > > > How can I find a acceptable model? Any suggestion will be appreciated !! > > > > I feel increasing the polarity of PVME maybe helpful. Is it right? > > > > Thanks in advance. > * > Ji Qing > Polymer Physics > Institute of Chemistry, Chinese Academy of Sciences > Tel: 0086-10-62562894 ，82618423 > * > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox using tip5p water results in too few number of water molecules
David, The results from using version 3.3.1 is different from version 3.3.2. In version 3.3.1, adding "SOL OL 0" and executing "genbox -cs tip5p.gro -box 1 1 1" created a box with 37 SOL molecules but the density is too high at 3072.87 g/L. In version 3.3.2, adding "SOL OL 0" did not work. However, I added "SOL LP0" to the end of vdwradii.dat and the resulting water box contained 37 SOL molecules. The density is incorrect at 2582.79 g/l. This box contains six more SOL molecules compared to a box created with TIP4P water. JW On 10/7/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > JW Feng wrote: > > Hello, > > > > I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC, > > TIP4P and TIP5P water with " > > genbox -cs .gro -box 1 1 1". The TIP5P box contains half > > the number of water molecules compared to TIP4P and SPC. > > SPC: 33 SOL molecules, density=987.205 (g/l) > > TIP4P: 31 SOL molecules > > TIP5P: 15 SOL molecules > > > > Can anyone please explain this? How do I get genbox to create a box > > with the right number of TIP5P water molecules. > > Thanks, > > > > JW > > > It is because of the name of the lone pairs (OL) which is interpreted as > an oxygen atom. You can add OL in vdwradii.dat with radius 0 and try > again. Please report whether it works, then I will fix it in further > releases. > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genbox using tip5p water results in too few number of water molecules
Hello, I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC, TIP4P and TIP5P water with " genbox -cs .gro -box 1 1 1". The TIP5P box contains half the number of water molecules compared to TIP4P and SPC. SPC: 33 SOL molecules, density=987.205 (g/l) TIP4P: 31 SOL molecules TIP5P: 15 SOL molecules Can anyone please explain this? How do I get genbox to create a box with the right number of TIP5P water molecules. Thanks, JW -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
