[gmx-users] Re: gmx-users Digest, Vol 114, Issue 75
Not working is too vague a symptom for anyone to guess what the problem is, sorry. Mark On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote: dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double- precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- Thanks Mark for your reply. Using the 500ps trajectory i want to calculate the number of hydrogen bonds as a function of time in vacuum .For this calculation i have uesd g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num hbond-num.xvg -dist dist.xvg -ang angle.xvg With what groups? Can there be any hydrogen bonds between those groups? Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a shorter trajectory work because it took less time? Does doing only one of three analyses help things to work? You'd be much closer to a solution if you'd tried some simplifications and done some detective work already ;-) Programm was running .After 1 hour it was still running but there was no output. If I calculate the number of hydrogen bonds as a function of time in water (no vacuum) using the same command line then there was no problem. Same problem when I used g_rdf in vacuum.The commad line I have used g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also checked with -nopbc with the same command line. RDF of what, in vacuum? What groups did you use? The programm is running but in the output file nothing is written. If I used g_rdf in water using the same command line there was no problem. OK - but does your analysis make sense in vacuum? Mark Thanks Mark for your reply In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I want to calculate the distance between O atom and N-H hydrogen atom using g_rdf in vacuum. Similarly using the same index file I want to calculate the number of hydrogen bonds as a function of time in vacuum using g_hbond. Yes there is a H bond between C=O oxygen atom of i-th residue and N-H hydrogen of i+4-th residue. I also checked with shorter trajectory there is also same problem . Please let me know If there are any mistakes. - santu -- 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] Re: gmx-users Digest, Vol 114, Issue 64
Not working is too vague a symptom for anyone to guess what the problem is, sorry. Mark On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote: dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double-precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- Thanks Mark for your reply. Using the 500ps trajectory i want to calculate the number of hydrogen bonds as a function of time in vacuum .For this calculation i have uesd g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num hbond-num.xvg -dist dist.xvg -ang angle.xvg Programm was running .After 1 hour it was still running but there was no output. If I calculate the number of hydrogen bonds as a function of time in water (no vacuum) using the same command line then there was no problem. Same problem when I used g_rdf in vacuum.The commad line I have used g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also checked with -nopbc with the same command line. The programm is running but in the output file nothing is written. If I used g_rdf in water using the same command line there was no problem. -- 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 and g_rdf in vacuum
dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double-precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- 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] SR-coulomb energy
Dear users,
I have performed an simulation of polypeptide(5-residues of
alanine) in vacuum using gmx_4.5.5 (Double Precision). For this, I am using
all cutoff=0 with no pbc. The input mdp file for the simulation is given
below
title= peptide in vaccum
cpp = /lib/cpp
define = -DFLEXIBLE
; RUN CONTROL
integrator = md
comm_mode = ANGULAR
nsteps = 100
dt = 0.0005
; NEIGHBOR SEARCHING
nstlist = 0
ns_type = simple
pbc = no
rlist = 0
; OUTPUT CONTROL
nstxout = 1000
nstvout = 1000
nstxtcout= 0
nstlog = 1000
constraints = none
nstenergy= 1000
; OPTION FOR ELECTROSTATIC AND VDW
rcoulomb = 0
; Method for doing Van der Waals
rvdw = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl = V-rescale
tc_grps = Protein
tau_t= 0.1
ref_t= 300
The output (.log) file is
Step Time Lambda
00.00.0
Group rest with mass 4.28491e+02, Ekrot 6.48028e+00 Det(I) = 4.27209e+03
COM: 1.82773 1.85017 1.82461
P:0.0 -0.0 0.0
V:0.0 -0.0 0.0
J: -0.82095 -13.54870 -19.02024
w:0.02012 -0.41432 -0.38715
Inertia tensor (3x3):
Inertia tensor[0]={ 1.34454e+01, -6.11374e+00, 2.21534e+00}
Inertia tensor[1]={-6.11374e+00, 2.88115e+01, -6.31417e+00}
Inertia tensor[2]={ 2.21534e+00, -6.31417e+00, 1.36527e+01}
Energies (kJ/mol)
Bond AngleProper Dih. Ryckaert-Bell. LJ-14
4.93368e+001.49038e+011.00713e+003.83183e+017.57789e+01
Coulomb-14LJ (SR) Coulomb (SR) PotentialKinetic En.
7.82758e+02 -6.47030e+01 -1.48187e+03 -6.28870e+022.30892e+02
Total Energy Conserved En.Temperature Pressure (bar)
-3.97978e+02 -3.97978e+023.08553e+020.0e+00
gen_vel = yes
gen_temp = 300
Now the problem is with Coulomb (SR) value.To check this value, I have
calculated coulomb interactions beyond 1-4 interaction by the following
equation
energ=(f*q1*q2)/r ; where f=138.935485
but the value which I obtain for step 0 is -170.10733 and this not the same
as the log file. I do not know how Gromacs calculate coulomb (SR) value.
Please suggest if I am missing something.
Thanks
Santu
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[gmx-users] Re: gmx-users Digest, Vol 105, Issue 43
thank you Justin.Now it is fine. -- Message: 1 Date: Wed, 9 Jan 2013 22:50:13 +0530 From: SANTU BISWAS santu.biswa...@gmail.com Subject: [gmx-users] energy-mimisation-problem To: gmx-users@gromacs.org Message-ID: caewz1z-7yv_8dcaurt+rm6fkdqomcmftxpdkbzl0atyyoor...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 dear users, I am performing an energy minimization of apolypeptide(formed by alanine-10-residues) in vacuum box by using Steepest Descent(initially) and then Conjugate Gradient methods in gromacs_4.5.5_doubleprecision.The chain length of alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range interactions.so i use cutoff 2.0 nm .But in the output (.log )file there is a contribution of energy for long-range interactions(in both energy minimisation methods). I do not understand why this is happening. the input file for energy minimisation is, ;title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; Input file integrator = steep/cg nsteps = 1 nstlist = 1 rlist = 1.0 rcoulomb= 2.0 rvdw= 2.0 ; Energy minimizing stuff emtol = 0.001 emstep = 0.1 nstcgsteep = 10 the output(.log )file is, Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 8.48244e+002.10205e+012.39409e+00 9.86941e+01 1.47894e+02 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 Potential Pressure (bar) -1.26841e+030.0e+00 santu -- Message: 2 Date: Wed, 09 Jan 2013 12:30:06 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] energy-mimisation-problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50eda91e.2070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 1/9/13 12:20 PM, SANTU BISWAS wrote: dear users, I am performing an energy minimization of apolypeptide(formed by alanine-10-residues) in vacuum box by using Steepest Descent(initially) and then Conjugate Gradient methods in gromacs_4.5.5_doubleprecision.The chain length of alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range interactions.so i use cutoff 2.0 nm .But in the output (.log )file there is a contribution of energy for long-range interactions(in both energy minimisation methods). I do not understand why this is happening. the input file for energy minimisation is, ;title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; Input file integrator = steep/cg nsteps = 1 nstlist = 1 rlist = 1.0 rcoulomb= 2.0 rvdw= 2.0 ; Energy minimizing stuff emtol = 0.001 emstep = 0.1 nstcgsteep = 10 You haven't set a value for the pbc keyword, so it takes the default value (xyz). The result is that you're not really minimizing in vacuo, but rather in some sort of pseudo-crystal state that probably has lots of periodicity artifacts. That's probably the source of the energy terms - your peptide interacting with itself. -Justin the output(.log )file is, Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 8.48244e+002.10205e+012.39409e+00 9.86941e+01 1.47894e+02 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 Potential Pressure (bar) -1.26841e+030.0e+00 santu -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] Re: energy-mimisation-problem
On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS santu.biswa...@gmail.com wrote: dear users, When performing a energy minimization of a polypeptide(formed by lysine-5-residues) in vacuum box by using Steepest Descent and also Conjugate Gradient methods in gromacs double precision,i noted that GROMACS never converges to emtol values under about 0.1 kj/mol/nm.I have used the .mdp file which is given below title= cpp = /lib/cpp ;include =-I../top/ define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 1000 rlist= 0.9 rcoulomb = 0.9 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 0.9 ; Neighbour searching nstlist = 1 ; ENERGY MINIMIZATION OPTIONS = emtol= 0.1 emstep = 0.1 nstcgsteep = 1000 santu -- 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
