[gmx-users] testing Tip5p water
Dear all,
a similar problem was proposed in this list in 2002:
http://www.gromacs.org/pipermail/gmx-users/2002-August/002339.html
I cannot solve my problem, when testing tip5p in gromacs.
T( c) density((g/cm^3) -E(kcal/mol)
REF125.0 0.999 9.8676
REF225.0 0.984 9.682
my results 25.0 0.984 -7.907
(data published (REF1:JCP 112, p8910 (2000)),
REF2: J. Chem. Phys. 117(19):8892-8897. (2002)) )
I want to what results in the big difference above.
my main parameters:
a.512 water molecules in NVT system from 1ns average collections
after 1ns equilibrium.
integrator = md
dt = 0.001
nstlist = 10
ns_type = grid
pbc = xyz
rlist= 1
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.22
DispCorr = Ener ;
fourierspacing = 0.12
pme_order= 6
Tcoupl = Berendsen
tau_t= 0.5
ref_t= 298
Thanks a lot in advance!
Yusong
//
PS: here is md0.log:
CPU= 0, lastcg= 127, targetcg= 383, myshift=2
CPU= 1, lastcg= 255, targetcg= 511, myshift=2
CPU= 2, lastcg= 383, targetcg= 128, myshift=2
CPU= 3, lastcg= 511, targetcg= 256, myshift=2
nsb-shift = 2, nsb-bshift= 0
Listing Scalars
nsb-nodeid: 0
nsb-nnodes: 4
nsb-cgtotal: 512
nsb-natoms: 2560
nsb-shift: 2
nsb-bshift: 0
Nodeid index homenr cgload workload
0 0 640 128 128
1 640 640 256 256
21280 640 384 384
31920 640 512 512
parameters of the run:
integrator = md
nsteps = 100
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 1500
nstxout = 250
nstvout = 250
nstfout = 250
nstenergy= 250
nstxtcout= 1000
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 24
nky = 24
nkz = 21
pme_order= 6
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bUncStart= FALSE
bShakeSOR= FALSE
etc = Berendsen
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
andersen_seed= 815131
rlist= 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.22
epsilon_r= 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = Ener
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
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
dihre-tau= 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
[gmx-users] how to make choices of COM in the system with freeze group?
Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of system as a whole. 4) do not use any COM How do I make the choices? I use gromacs program 3.3.3 Thank you very much!!! Yusong. ___ 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] Warning message with 3.3.3 but not with 3.3.1
Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 ___ 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] Warning message with 3.3.3 but not with 3.3.1
David wrote: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Thank you for replying. Do you mean, that it must be nothing when system has any freeze groups? Yusong. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 4:01 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 tuyusong wrote: Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 ___ 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] how to make choices of COM in the system with freeze group?
You can opt for 3). If your system only compose of nanotube and water, why freeze it? Thank Yang Ye, we are doing some tests on effects of T-coupling caused by removing COM in the system with freeze groups Regards, Yusong tuyusong wrote: Hi, all, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 3) only remove the COM of system as a whole. 4) do not use any COM How do I make the choices? I use gromacs program 3.3.3 Thank you very much!!! Yusong. ___ 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 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 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] Warning message with 3.3.3 but not with 3.3.1
Bo wrote: Thanks David. So to speak, as the center of mass of group SOL is not free to move, we do not need stopcm to it. Another question is, does it would be problematic in long time simulation without stopcm in such situation, I mean the systematic errors caused by center of mass motion. Thanks for clarification. For a system with freeze group, we should not use any removal of com motions, and this system should still work. I don't find this relevant descriptions in gmx-manual, and it may be added into it. Yusong tuyusong wrote: Even in the system with position-restrain, when only removing com of SOL group, gmx 3.3.3 also give the same error information as Bo: you can not only remove the com motion of one group. it is all (in one or more groups) or nothing. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: Inf Yusong -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, April 17, 2008 3:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Warning message with 3.3.3 but not with 3.3.1 Bo Zhou wrote: Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. stopcm tries to change the velocity of the rest group (solid) as well. Unfortunately you can not turn this off for one group. I'm not sure while this is different from 3.3.1, but since you have a solid reference you probably don't need to stopcm. ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 48, Issue 48 *** ___ 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 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] how to make choices of COM in the system with freeze group
Hi, Users, I have a system with one carbon Nanotube and lots of water, in which Nanotube is frozen. How do I remove the center-of-mass: 1) only remove the COM of SOL 2) remove both COM of SOL and CNT, separately 2) only remove the COM of system as a whole. How do I make the choices? Thank you very much!!! Yusong. - ___ 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
