Re: [gmx-users] Re: Different energy using the identical tpr file
Hi thanks for your reply, and sorry to be late since I am living 9 hours
behind you :)
I tried but still I get different energies. I check tpr files, according to
gmxcheck they are identical ...
But they give me different energies in different computers...
here is what I do:
$Mygrompp -f nvt.mdp -c out.pdb -p gromacs-complex-dman-par.top -o test0.tpr
$Mymdrun -deffnm test0 -s test0.tpr -rerun out.pdb -reprod
rm -f *.xvg
echo 10 0 | $Mygenergy -f test0.edr -o energy.xvg
cat energy.xvg | tail -1 | awk '{print $2}' Out-enegy
And this is the content of nvt.mdp
title= polyala
cpp = /usr/bin/cpp
integrator = md
comm_mode= Linear
dt = 0.002
nsteps = 0
nstxout = 1
nstvout = 1
nstlog = 1
nstenergy= 1
nstxtcout= 1
xtc-precision= 1000
energygrps = System
pbc = xyz
nstlist = 10
ns_type = grid
rlist= 0.9
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.12
pme_order= 4
ewald_rtol = 1e-5
epsilon_r= 1.0
optimize_fft = yes
vdwtype = Cut-off
rvdw = 0.9
; T coupling
tcoupl = Nose-Hoover
tc-grps = System
tau_t= 1
ref_t= 300.0
; P coupling
pcoupl = no
pcoupltype = isotropic
tau_p= 1
compressibility = 4.5e-5
ref_p= 1.0
; Velocity generation
gen_vel = no
gen_temp = 350.0
gen_seed = 13200
; Constraints bonds
constraints = all-bonds
constraint_algorithm = lincs
lincs-order = 4
lincs-warnangle = 30
user1-grps = System
On Fri, Apr 19, 2013 at 6:15 AM, Andrish Reddy are...@csir.co.za wrote:
Have you tried the -reprod option?
Andrish
Fahimeh Baftizadeh wrote
Hello,
I have a 2 tpr files which are identical. Then I am doing a single step
MD
(I put n_step=0) simulation just to compute the total energy of a certain
configuration.
These tpr files give me different energy values ... when I run it on my
computer or on another computer. Even the gromacs version is the same in
both computers. I compiled gromacs identical in both computers.
Can you help me to figure it out?
Thanks
Fahimeh
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Re: [gmx-users] Re: Different energy using the identical tpr file
Dear Mark,
Thanks for the pages.
Now it is clear to me that because the shared libraries maybe are not
identical during compilation, I am getting different value for energies.
However, I have to perform single point energy calculation for a lot of
structure and the only thing that I care about is the energy difference. I
have checked the energy difference that I get in different computers ...
casue I thought that maybe the difference is identical. However this is not
the case as well ...
May I have your comment about it?
E2-E1(computer1)= 83801.086088
E2-E1(computer2)= 8366.248918
As you see the order of magnitude is even different !
Could you please help me to understand this better
Thanks
Fahimeh
On Fri, Apr 19, 2013 at 9:01 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Apr 19, 2013 2:50 PM, Fahimeh Baftizadeh
fahimeh.baftiza...@googlemail.com wrote:
Hi thanks for your reply, and sorry to be late since I am living 9 hours
behind you :)
I tried but still I get different energies. I check tpr files, according
to
gmxcheck they are identical ...
But they give me different energies in different computers...
I didn't write and link those pages for my own benefit ;-)
Mark
here is what I do:
$Mygrompp -f nvt.mdp -c out.pdb -p gromacs-complex-dman-par.top -o
test0.tpr
$Mymdrun -deffnm test0 -s test0.tpr -rerun out.pdb -reprod
rm -f *.xvg
echo 10 0 | $Mygenergy -f test0.edr -o energy.xvg
cat energy.xvg | tail -1 | awk '{print $2}' Out-enegy
And this is the content of nvt.mdp
title= polyala
cpp = /usr/bin/cpp
integrator = md
comm_mode= Linear
dt = 0.002
nsteps = 0
nstxout = 1
nstvout = 1
nstlog = 1
nstenergy= 1
nstxtcout= 1
xtc-precision= 1000
energygrps = System
pbc = xyz
nstlist = 10
ns_type = grid
rlist= 0.9
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.12
pme_order= 4
ewald_rtol = 1e-5
epsilon_r= 1.0
optimize_fft = yes
vdwtype = Cut-off
rvdw = 0.9
; T coupling
tcoupl = Nose-Hoover
tc-grps = System
tau_t= 1
ref_t= 300.0
; P coupling
pcoupl = no
pcoupltype = isotropic
tau_p= 1
compressibility = 4.5e-5
ref_p= 1.0
; Velocity generation
gen_vel = no
gen_temp = 350.0
gen_seed = 13200
; Constraints bonds
constraints = all-bonds
constraint_algorithm = lincs
lincs-order = 4
lincs-warnangle = 30
user1-grps = System
On Fri, Apr 19, 2013 at 6:15 AM, Andrish Reddy are...@csir.co.za
wrote:
Have you tried the -reprod option?
Andrish
Fahimeh Baftizadeh wrote
Hello,
I have a 2 tpr files which are identical. Then I am doing a single
step
MD
(I put n_step=0) simulation just to compute the total energy of a
certain
configuration.
These tpr files give me different energy values ... when I run it on
my
computer or on another computer. Even the gromacs version is the same
in
both computers. I compiled gromacs identical in both computers.
Can you help me to figure it out?
Thanks
Fahimeh
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If you torture the data long
[gmx-users] Different energy using the identical tpr file
Hello, I have a 2 tpr files which are identical. Then I am doing a single step MD (I put n_step=0) simulation just to compute the total energy of a certain configuration. These tpr files give me different energy values ... when I run it on my computer or on another computer. Even the gromacs version is the same in both computers. I compiled gromacs identical in both computers. Can you help me to figure it out? Thanks Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] file.itp for separated molecules
Hello I have to question. 1- I am generating a gro and toplogy file from a pdb file, usign pdb2gmx. the pdb file contains 18 separate chains, in each chain, there are 6 residues. When I generate the topology and coordinates, it creates 18 posres-protein$i.itp file and 18 topol-protein$i.itp file and then one topol.top and one conf.gro ... is it normal? i think it is just the position restraint for separate chains ... in this way i think it enables me to restraint them separately if i want? right? 2- using topol.top and conf.gro, after solvating the molecule in the box of water ... with editconf and genbox ... I am trying to generate a tpr file, but when it generate it writes the following: Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'Protein2' Excluding 3 bonded neighbours molecule type 'Protein3' Excluding 3 bonded neighbours molecule type 'Protein4' Excluding 3 bonded neighbours molecule type 'Protein5' Excluding 3 bonded neighbours molecule type 'Protein6' Excluding 3 bonded neighbours molecule type 'Protein7' Excluding 3 bonded neighbours molecule type 'Protein8' Excluding 3 bonded neighbours molecule type 'Protein9' Excluding 3 bonded neighbours molecule type 'Protein10' Excluding 3 bonded neighbours molecule type 'Protein11' Excluding 3 bonded neighbours molecule type 'Protein12' Excluding 3 bonded neighbours molecule type 'Protein13' Excluding 3 bonded neighbours molecule type 'Protein14' Excluding 3 bonded neighbours molecule type 'Protein15' Excluding 3 bonded neighbours molecule type 'Protein16' Excluding 3 bonded neighbours molecule type 'Protein17' Excluding 3 bonded neighbours molecule type 'Protein18' Excluding 2 bonded neighbours molecule type 'SOL' what is this telling me? I didn't find a solution searching in the mailing list?! Thanks Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] mpirun
Hello, I am using Metadynamics implemented on gromacs, doing normal one dimentional test on a simple system. I see the results of using only one processor or more than one processors are different. always I use the same tpr starting file, So, is it normal to have different results (in my case different value of collective varriables) in the beggining they are exactely equal but after some steps, they diverge ! Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Fw: mpirun
sorry I forgot to add that the random seed for the velocity is the same in all the tprs and the random seed for the thermostat is also the same. and if I redo the simulation with only one processor, the results are always identical. but not with more than one. Do you think is it due to the comunication of the processors together?! Thanks Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] rerun on gro file
Hi, I'm trying to do rerun on a trajectory which came from catting some gro files of a metadynamics simulation. I simply did trjcat -f 1.gro 2.gro 3.gro -o all.xtc -cat then I used this all.xtc for rerun. the output COLVAR is written but only for one step, I did test on some other trajectory and I am sure that META_INP.dat which is the input of metadynamics is correct. I dont know if the problem is catting the gro file ?!! Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] rerun on gro file
Thank you Justin, I used -settime option and set different starting time, at the end I check xtc file with gmxcheck and the number of fram is ok. But I still have the same problem, I copy what is inside the log file: Step Time Lambda 0 0.0 0.0 Grid: 9 x 9 x 9 cells Energies (kJ/mol) Angle Proper Dih. LJ-14 Coulomb-14 LJ (SR) 5.86630e+03 5.17677e+03 3.00597e+03 1.71532e+04 3.14231e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -2.38136e+05 -7.84053e+04 -2.53916e+05 0.0e+00 -2.53916e+05 Temperature Pressure (bar) Cons. rmsd () 0.0e+00 1.62084e+04 0.0e+00 Step Time Lambda 0 50.0 0.0 Energies (kJ/mol) Angle Proper Dih. LJ-14 Coulomb-14 LJ (SR) 5.76066e+03 5.05958e+03 2.98882e+03 1.71326e+04 3.15995e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -2.39283e+05 -7.85130e+04 -2.55255e+05 0.0e+00 -2.55255e+05 Temperature Pressure (bar) Cons. rmsd () 0.0e+00 1.61866e+04 0.0e+00 Step Time Lambda 0 100.0 0.0 Energies (kJ/mol) Angle Proper Dih. LJ-14 Coulomb-14 LJ (SR) 5.87814e+03 5.08816e+03 3.04501e+03 1.72935e+04 3.20109e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -2.38788e+05 -7.85518e+04 -2.54024e+05 0.0e+00 -2.54024e+05 Temperature Pressure (bar) Cons. rmsd () 0.0e+00 1.62936e+04 0.0e+00 Step is always zero !!! do you think is this the problem ?!! Fahimeh --- On Sat, 9/18/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] rerun on gro file To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, September 18, 2010, 10:51 PM fahimeh baftizadeh wrote: Hi, I'm trying to do rerun on a trajectory which came from catting some gro files of a metadynamics simulation. I simply did trjcat -f 1.gro 2.gro 3.gro -o all.xtc -cat then I used this all.xtc for rerun. the output COLVAR is written but only for one step, I did test on some other trajectory and I am sure that META_INP.dat which is the input of metadynamics is correct. I dont know if the problem is catting the gro file ?!! Probably. Use -settime to assign times to each of the frames, otherwise they may all be set to something like 0 or -1. You can use gmxcheck on the .xtc file to see what Gromacs thinks it contains. -Justin Fahimeh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
hello, I have a trajectory generated by gromacs in which I excluded water and there is only protein, now I like to see how does the number of h_bond between water and protein change during the trajectory. In fact when I use g_hbond I can choose the water and protein but I was wondering where does the information about water come from?? thank you in advance for your time Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_hbond
Thanks for the reply. In fact I had the trajectory with water but then I removed it to have smaller size of files. the point is that It didn't complain or crash when I was using that trajectory, choosing water in the groups selecting. but it didn't also generate any output. that is why I asked that ... Anyway since I have gro files time to time, I think I will cat all the gro file and use that for analysis of h_bond. Fahimeh --- On Fri, 9/17/10, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] g_hbond To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, September 17, 2010, 9:37 PM On 9/17/10 5:37 PM, Justin A. Lemkul wrote: Fahimeh Baftizadeh Baghal wrote: hello, I have a trajectory generated by gromacs in which I excluded water and there is only protein, now I like to see how does the number of h_bond between water and protein change during the trajectory. In fact when I use g_hbond I can choose the water and protein but I was wondering where does the information about water come from?? Certainly you can choose whatever groups are present (either from default groups or from those in an index file), but I would imagine the command will either fail or simply identify that there are no hydrogen bond donors or acceptors within what would otherwise be water. If you have not saved the coordinates for water, you cannot run any command to analyze properties related to or involving water. In theory you could get an approximate number from analyzing what polar groups are not hydrogen bonded intramolecularly. There is not ready tool to do this. The quickest solution is probably to rerun the simulation. In most cases human time is more valuable than computer time. -Justin thank you in advance for your time Fahimeh -- David. David van der Spoel, PhD, Professor of Biology 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 sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] strange jumping in the frames
I am running Metadynamics with gromacs, I saw a jump in the frame after the simulation was running for a while, I copy here part of the log file: Step Time Lambda 2055750041115.00.0 Energies (kJ/mol) AngleProper Dih. LJ-14 Coulomb-14LJ (SR) 3.54705e+032.44201e+031.44990e+031.94769e+042.63535e+04 Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy -2.09459e+05 -5.86065e+04 -2.14796e+055.09371e+04 -1.63859e+05 Conserved En.Temperature Pressure (bar) Cons. rmsd () -1.66948e+053.47266e+02 -2.03134e+022.74833e-05 DD step 2055 vol min/aver 0.846 load imb.: force 0.4% Step Time Lambda 205641120.00.0 Energies (kJ/mol) AngleProper Dih. LJ-14 Coulomb-14LJ (SR) 3.36185e+032.48355e+031.45350e+031.94714e+042.67211e+04 Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy -2.09297e+05 -5.86137e+04 -2.14420e+055.18801e+04 -1.62540e+05 Conserved En.Temperature Pressure (bar) Cons. rmsd () -1.67082e+053.53695e+027.73024e+012.66928e-05 DD step 20562499 vol min/aver 0.825 load imb.: force 0.6% Step Time Lambda 2056250041125.003910.0 Energies (kJ/mol) AngleProper Dih. LJ-14 Coulomb-14LJ (SR) 3.55493e+032.49077e+031.45219e+031.93942e+042.60391e+04 Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy -2.08596e+05 -5.86454e+04 -2.14310e+055.14416e+04 -1.62868e+05 Conserved En.Temperature Pressure (bar) Cons. rmsd () -1.67250e+053.50706e+02 -3.50552e+022.93757e-05 as you can see the time jumped from 41120.0 to 41125.00391 , while it has to be 41125.0 and then it continue the rest of simulation like this, Do you what is the problem ?!! Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
