[gmx-users] Turn-off water optimisation
Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Turn-off water optimisation
Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Turn-off water optimisation
Hi, i have the following problem: (GROMACS 4.0.5) when i simulated water in serial on our cluster with the brendsen or v-rescale thermostat i get to high temperatures (300 K goes in very short time up to around 425 K). If i simulate in parallel or at my local machine i get no problems. Also if i change water to another molecule there are no such problems. (I use the same mdp file for all the simulations). Because the problem appears with water (spc and tip4p) but not with mesitylene i thought probably the special things for water (settle, and so on) could be the problem. So i wanted to simulate water without that fancy stuff. Thanks for the info with the enviroment variable, but where can i set it? For the other problems (why it works on the cluster in parallel, but not in serial, but works on the local-pc in serial) i have so far no idea, where to look. But first i'm happy to know if the problem comes from the special water-loops. Thomas Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schlesi at uni-mainz.de To: gmx-users at gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing list gmx-users at gromacs.org http://lists.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 gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Turn-off water optimisation
Hi, I have never heard about problems like this before. It seems highly unlikely to me that the innerloops are causing this. Are your running exacly the same tpr file on your local machine and the cluster? You probably want to update to version 4.0.7 to be sure you have all the latest bugfixes. Please keep us updated on this issue, since things like this should never happen (unless there is a compiler bug). Berk Date: Fri, 5 Mar 2010 14:41:02 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] Turn-off water optimisation Hi, i have the following problem: (GROMACS 4.0.5) when i simulated water in serial on our cluster with the brendsen or v-rescale thermostat i get to high temperatures (300 K goes in very short time up to around 425 K). If i simulate in parallel or at my local machine i get no problems. Also if i change water to another molecule there are no such problems. (I use the same mdp file for all the simulations). Because the problem appears with water (spc and tip4p) but not with mesitylene i thought probably the special things for water (settle, and so on) could be the problem. So i wanted to simulate water without that fancy stuff. Thanks for the info with the enviroment variable, but where can i set it? For the other problems (why it works on the cluster in parallel, but not in serial, but works on the local-pc in serial) i have so far no idea, where to look. But first i'm happy to know if the problem comes from the special water-loops. Thomas Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schlesi at uni-mainz.de To: gmx-users at gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing list gmx-users at gromacs.org http://lists.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 gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Turn-off water optimisation
Hi, Can you also post your .mdp? Ran Berk Hess wrote: Hi, I have never heard about problems like this before. It seems highly unlikely to me that the innerloops are causing this. Are your running exacly the same tpr file on your local machine and the cluster? You probably want to update to version 4.0.7 to be sure you have all the latest bugfixes. Please keep us updated on this issue, since things like this should never happen (unless there is a compiler bug). Berk Date: Fri, 5 Mar 2010 14:41:02 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] Turn-off water optimisation Hi, i have the following problem: (GROMACS 4.0.5) when i simulated water in serial on our cluster with the brendsen or v-rescale thermostat i get to high temperatures (300 K goes in very short time up to around 425 K). If i simulate in parallel or at my local machine i get no problems. Also if i change water to another molecule there are no such problems. (I use the same mdp file for all the simulations). Because the problem appears with water (spc and tip4p) but not with mesitylene i thought probably the special things for water (settle, and so on) could be the problem. So i wanted to simulate water without that fancy stuff. Thanks for the info with the enviroment variable, but where can i set it? For the other problems (why it works on the cluster in parallel, but not in serial, but works on the local-pc in serial) i have so far no idea, where to look. But first i'm happy to know if the problem comes from the special water-loops. Thomas Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schlesi at uni-mainz.de To: gmx-users at gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing list gmx-users at gromacs.org http://lists.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 gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Turn-off water optimisation
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 703303
cos_accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf:7101
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc:0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM= FALSE
QMconstraints= 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
*snip*
Using a Gaussian width (1/beta) of 0.448228 nm for Ewald
Cut-off's: NS: 1.4 Coulomb: 1.4 LJ: 1.4
System total charge: 0.000
Generated table with 1200 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 1184 molecules.
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Removing pbc first time
*snip*
There are: 3552 Atoms
Max number of connections per atom is 2
Total number of connections is 4736
Max number of graph edges per atom is 2
Total number of graph edges is 4736
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 303.041 K
Started mdrun on node 0 Thu Mar 4 11:20:10 2010
Step Time Lambda
00.00.0
Grid: 6 x 4 x 4 cells
Long Range LJ corr.: C6 2.9082e-04
Long Range LJ corr.: Epot -77.7923, Pres: -71.7651, Vir:77.7923
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
1.13442e+04 -7.77923e+01 -7.05664e+04 -1.53951e+03 -6.08396e+04
Kinetic En. Total Energy Conserved En.Temperature Pressure (bar)
8.93685e+03 -5.19027e+04 -5.18779e+043.02732e+02 -2.59307e+03
Step Time Lambda
25005.00.0
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
6.18686e+03 -7.77923e+01 -4.50870e+04 -1.36173e+03 -4.03397e+04
Kinetic En. Total Energy Conserved En.Temperature Pressure (bar)
1.25168e+04 -2.78229e+041.22037e+054.24002e+022.25670e+03
*snip*
== ### ==
A V E R A G E S
== ### ==
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
6.15659e+03 -7.77923e+01 -4.59217e+04 -1.32129e+03 -4.11642e+04
Kinetic En. Total Energy Conserved En.Temperature Pressure (bar)
1.26205e+04 -2.85438e+049.37069e+064.27512e+021.82506e+03
Greetings
Thomas
Hi,
Can you also post your .mdp?
Ran
Berk Hess wrote:
Hi,
I have never heard about problems like this before.
It seems highly unlikely to me that the innerloops are causing this.
Are your running exacly the same tpr file on your local machine
and the cluster?
You probably want to update to version 4.0.7 to be sure you have
all the latest bugfixes.
Please keep us updated on this issue, since things like this should
never happen (unless there is a compiler bug).
Berk
Date: Fri, 5 Mar 2010 14:41:02 +0100
From: schl...@uni-mainz.de
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Turn-off water optimisation
Hi,
i have the following problem: (GROMACS 4.0.5)
when i simulated water in serial on our cluster
RE: [gmx-users] Turn-off water optimisation
Hi all, to summerize the seems really like a compiler problem. i have now compiled 4.0.5 with gcc and had no problems. i don't really know which icc compiler it was (but had send the guy who installed gromacs a mail), but with 'which icc' i find: /share/apps/intel/cce/9.1.046/bin/icc i will try now 4.0.7 with the icc compiler Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
