[gmx-users] select groups in g_rms
Dear Sir, When I run g_rms -s md.tpr -f md.trr -o rmsd.xvg, the program requires me selecting a group twice as following: g_rms -s md.tpr -f md.trr -o rmsd.xvg后, 程序两次要求选结构组,如下: Reading file md.tpr, VERSION 3.3.1 (single precision) Reading file md.tpr, VERSION 3.3.1 (single precision) Select group for least squares fit Opening library file /home/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Group 0 ( System) has 519889 elements Group 1 ( Protein) has 24649 elements Group 2 ( Protein-H) has 12688 elements Group 3 ( C-alpha) has 1540 elements Group 4 ( Backbone) has 4620 elements Group 5 ( MainChain) has 6172 elements Group 6 (MainChain+Cb) has 7620 elements Group 7 ( MainChain+H) has 7668 elements Group 8 ( SideChain) has 16981 elements Group 9 ( SideChain-H) has 6516 elements Group 10 ( Prot-Masses) has 24649 elements Group 11 ( Non-Protein) has 495240 elements Group 12 ( SOL) has 495240 elements Group 13 ( Other) has 495240 elements Select a group: 1 Selected 1: 'Protein' Select group for RMSD calculation Opening library file /home/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Group 0 ( System) has 519889 elements Group 1 ( Protein) has 24649 elements Group 2 ( Protein-H) has 12688 elements Group 3 ( C-alpha) has 1540 elements Group 4 ( Backbone) has 4620 elements Group 5 ( MainChain) has 6172 elements Group 6 (MainChain+Cb) has 7620 elements Group 7 ( MainChain+H) has 7668 elements Group 8 ( SideChain) has 16981 elements Group 9 ( SideChain-H) has 6516 elements Group 10 ( Prot-Masses) has 24649 elements Group 11 ( Non-Protein) has 495240 elements Group 12 ( SOL) has 495240 elements Group 13 ( Other) has 495240 elements Select a group: 3 Selected 3: 'C-alpha' trn version: GMX_trn_file (single precision) Last frame 100 time 100.000 I don't understand how to make the first selction Select group for least squares fit, and the secend select Select group for RMSD calculation, and I don't understand the meaning of these selection. I hope you can help me. Thanks. Best regards! Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china-- 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] select groups in g_rms
You could start by reading the gromacs manual, Section 8.9 On 12/20/11 9:30 AM, yp sun wrote: Dear Sir, When I run g_rms -s md.tpr -f md.trr -o rmsd.xvg, the program requires me selecting a group twice as following: g_rms -s md.tpr -f md.trr -o rmsd.xvg?, ??? ? ??,??: Reading file md.tpr, VERSION 3.3.1 (single precision) Reading file md.tpr, VERSION 3.3.1 (single precision) Select group for least squares fit Opening library file /home/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Group 0 ( System) has 519889 elements Group 1 ( Protein) has 24649 elements Group 2 ( Protein-H) has 12688 elements Group 3 ( C-alpha) has 1540 elements Group 4 (Backbone) has 4620 elements Group 5 ( MainChain) has 6172 elements Group 6 (MainChain+Cb) has 7620 elements Group 7 ( MainChain+H) has 7668 elements Group 8 ( SideChain) has 16981 elements Group 9 ( SideChain-H) has 6516 elements Group10 ( Prot-Masses) has 24649 elements Group11 ( Non-Protein) has 495240 elements Group12 ( SOL) has 495240 elements Group13 ( Other) has 495240 elements Select a group: 1 Selected 1: 'Protein' Select group for RMSD calculation Opening library file /home/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Group 0 ( System) has 519889 elements Group 1 ( Protein) has 24649 elements Group 2 ( Protein-H) has 12688 elements Group 3 ( C-alpha) has 1540 elements Group 4 (Backbone) has 4620 elements Group 5 ( MainChain) has 6172 elements Group 6 (MainChain+Cb) has 7620 elements Group 7 ( MainChain+H) has 7668 elements Group 8 ( SideChain) has 16981 elements Group 9 ( SideChain-H) has 6516 elements Group10 ( Prot-Masses) has 24649 elements Group11 ( Non-Protein) has 495240 elements Group12 ( SOL) has 495240 elements Group13 ( Other) has 495240 elements Select a group: 3 Selected 3: 'C-alpha' trn version: GMX_trn_file (single precision) Last frame100 time 100.000 I don't understand how to make the first selction Select group for least squares fit, and the secend select Select group for RMSD calculation, and I don't understand the meaning of these selection. I hope you can help me. Thanks. Best regards! Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- Gianluca Santoni, Structural Protein Dynamics Research Team Institut de Biologie Structurale 41 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- 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] EM curve question
Dear GMX-users I am working on lipid-drug system.I have done these stages: 1.creating topology for drug and lipid 2.solvation 3.Ion addition 4.Energy minimization 5.NVT My question is,why does the energy and temperature curves converge to zero(I have used 320 K for my temperature in mdp file)? Thanks a lot in advance. P.Haghighi -- 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] regarding rtp file
hello sir, i go through the manual and your link.. i need to add BFC residue type in rtp file and residuetype.dat.. thing is i need to include charges angles bonds dihedrals impropers for residue in my rtp file ,, i dono how to define its value.. mine is 14 carbon fattyacid..(BFC) give some idea to define my residue,, thanking you, -- 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] Normal Mode Analysis starting from an optimized geometry and known partial charges
Dear GROMACS users,
I have done Normal Mode Analysis and have calculated partial charges and
the optimized geometry of a few compounds using high-level QM calculations.
Now I want to see (if possible) how well GROMACS can reproduce the normal
modes if I start from the same optimized geometry and use the same partial
charges. The command lines I use are the following:
ligand=10058_F4.nw.new_GMX
## do Normal Mode Analysis
grompp_d4.5.5 -f nm.mdp -c ${ligand}.gro -p ${ligand}.top -o nm.tpr
mdrun_d4.5.5 -v -deffnm nm
## calculate the eigenvectors/values of the Hessian matrix and write the
eigenvectors to a trajectory file
g_nmeig_d4.5.5 -f nm.mtx -s nm.tpr -of -ol -v -m -last 81
## plot the vector components and the RMS fluctuation per atom of
eigenvectors for all eigenvectors
echo 0 | g_anaeig_d4.5.5 -v eigenvec.trr -s nm.tpr -eig eigenval.xvg -comp
-rmsf -last -1
## create a trajectory from the eigenvector 76 (the first 6 are the
rotation and translation) to visualize the vibrations in VMD
g_nmtraj_d4.5.5 -s nm.tpr -v eigenvec.trr -eignr 76 -nframes 10
-amplitude 1 -o
Most of the resulting normal modes do not coincide with the respective ones
calculated through QM. Does the order of the above command lines make sense?
An obvious problem is that the starting compound geometry is not in full
precision as highlighted in the documentation:
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
Is it possible to create a full precision .trr coordinate file from a .gro
or any other structure file with modified 8-decimal point coordinates?
I am looking forward for an answer,
Thomas
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[gmx-users] Possible typo in nb_kernel_x86_64_sse.c (4.5.5)
Hi Devs, Is this intended or just a typo: #nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.c# .: 211:fprintf(log,Testing x86_64 SSE2 support...); .: ## instead of: .: 211:fprintf(log,Testing x86_64 SSE1 support...); .: The same thing appears in other _sse.c files. Thanks, Daniel -- 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] regarding rtp file
On 20/12/11, priya thiyagarajan priya.thiyagaraja...@gmail.com wrote: hello sir, i go through the manual and your link.. i need to add BFC residue type in rtp file and residuetype.dat.. thing is i need to include charges angles bonds dihedrals impropers for residue in my rtp file ,, i dono how to define its value.. mine is 14 carbon fattyacid..(BFC) give some idea to define my residue,, Actually with such species it is usually more a matter of choosing which atom types should be used for which atom, which usually determines the above parameters, which will then be looked up automatically, just as for the other .rtp entries. Parameters probably already exist in your force field for a fatty acid, and if they don't, that's probably a good reason to choose another force field. Mark -- 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] Normal Mode Analysis starting from an optimized geometry and known partial charges
On 20/12/11, Thomas Evangelidis teva...@gmail.com wrote:
Dear GROMACS users,
I have done Normal Mode Analysis and have calculated partial charges and the
optimized geometry of a few compounds using high-level QM calculations. Now I
want to see (if possible) how well GROMACS can reproduce the normal modes if
I start from the same optimized geometry and use the same partial charges.
In general for NMA to make sense you need to be at a stationary point w.r.t.
the atomic degrees of freedom of the model being used. That won't be quite true
at a QM geometry, so there's a sense of apples-vs-oranges comparison.
The command lines I use are the following:
ligand=10058_F4.nw.new_GMX
## do Normal Mode Analysis
grompp_d4.5.5 -f nm.mdp -c ${ligand}.gro -p ${ligand}.top -o nm.tpr
mdrun_d4.5.5 -v -deffnm nm
## calculate the eigenvectors/values of the Hessian matrix and write the
eigenvectors to a trajectory file
g_nmeig_d4.5.5 -f nm.mtx -s nm.tpr -of -ol -v -m -last 81
## plot the vector components and the RMS fluctuation per atom of
eigenvectors for all eigenvectors
echo 0 | g_anaeig_d4.5.5 -v eigenvec.trr -s nm.tpr -eig eigenval.xvg -comp
-rmsf -last -1
## create a trajectory from the eigenvector 76 (the first 6 are the rotation
and translation) to visualize the vibrations in VMD
g_nmtraj_d4.5.5 -s nm.tpr -v eigenvec.trr -eignr 76 -nframes 10 -amplitude
1 -o
Most of the resulting normal modes do not coincide with the respective ones
calculated through QM. Does the order of the above command lines make sense?
An obvious problem is that the starting compound geometry is not in full
precision
The starting geometry is in full precision if it's the same as that used for
the QM calculation. That is quite possible to achieve with .pdb or .gro input.
as highlighted in the documentation:
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
Is it possible to create a full precision .trr coordinate file from a .gro or
any other structure file with modified 8-decimal point coordinates?
I think you are misunderstanding the use of the word precision here. In
general, the same configuration will be represented differently in .trr and
.gro formats, with the former being a closer approximation. Accordingly, one
will get a different result for NMA on the endpoint of GROMACS EM as observed
in the .trr file and as observed in the .gro file. The former will be closer to
the stationary point, and so lead to more acceptable estimates of the normal
modes. However, here you want to do NMA on the same coordinates with two
programs, so it is up to you to represent the coordinates in a way that the two
programs can compute on the same approximation to the coordinates of the
stationary point. There's no need to convert to .trr (or the QM binary format),
because all that does is treat 2.613 as 2.613.
Mark
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Re: [gmx-users] EM curve question
On 20/12/11, parto haghighi parto.haghi...@gmail.com wrote: Dear GMX-users I am working on lipid-drug system.I have done these stages: 1.creating topology for drug and lipid 2.solvation 3.Ion addition 4.Energy minimization 5.NVT My question is,why does the energy and temperature curves converge to zero(I have used 320 K for my temperature in mdp file)? You've done something wrong, but on the available information we can't tell if you aren't modelling what you think you're modelling, or aren't observing what you think you're observing, or both. Mark -- 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: LINCS error
i went through the mailing list, but i dont understand when i run the same protein on my computer it runs correctly without any LINCS warning. On the cluster with 64 processors the job runs but crashes in between and shows the LINCS warning. Please anyone tell me what could be the reason. Is anything wrong with my protein. On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc= xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout= 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title= Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help. Thanks, Aiswarya -- 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] Re: LINCS error
On 20/12/11, aiswarya pawar aiswarya.pa...@gmail.com wrote: i went through the mailing list, but i dont understand when i run the same protein on my computer it runs correctly without any LINCS warning. On the cluster with 64 processors the job runs but crashes in between and shows the LINCS warning. That happens. Your different computers are running different versions of the calculation. Numerical artefacts do happen, especially if you use algorithms that are known to be unstable when not in equilibrium, like I said three days ago. Why have you repeated your question instead of trying my suggestion? Please anyone tell me what could be the reason. Is anything wrong with my protein. Something is very likely wrong with your system preparation. The links people have been giving you detail the advice on how to diagnose the problem or how to be more gentle. There's little else for me to say. Mark On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, I did energy minimization of a protein complex using the following minimization mdp file. ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 10; Write energies to disk every nstenergy steps energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) and the pr.mdp = ; VARIOUS PREPROCESSING OPTIONS title = Position Restrained Molecular Dynamics define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = -1 and md.mdp file = ; VARIOUS PREPROCESSING OPTIONS title = Position Restrained Molecular Dynamics ; RUN CONTROL PARAMETERS constraints = all-bonds integrator = md dt = 0.002 ; 2fs ! nsteps = 250 ; total 5000 ps. nstcomm = 10 nstxout = 500 ; collect data every 1 ps nstxtcout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes DispCorr = no ; Berendsen temperature coupling
Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges
Mark, thanks for the prompt response!
I have done Normal Mode Analysis and have calculated partial charges and
the optimized geometry of a few compounds using high-level QM calculations.
Now I want to see (if possible) how well GROMACS can reproduce the normal
modes if I start from the same optimized geometry and use the same partial
charges.
In general for NMA to make sense you need to be at a stationary point
w.r.t. the atomic degrees of freedom of the model being used. That won't be
quite true at a QM geometry, so there's a sense of apples-vs-oranges
comparison.
If I get it right you mean that NMA in GROMACS must start from an energy
minimum (stationary point) w.r.t the ff used (GAFF in my case), which means
that an energy minimization is neccessary ever if I use an QM optimum
geometry and the respective partial charges. Namely there is no way to
reproduce the normal modes I obtained from QM calculations, correct?
An obvious problem is that the starting compound geometry is not in full
precision
The starting geometry is in full precision if it's the same as that used
for the QM calculation. That is quite possible to achieve with .pdb or .gro
input.
The same as the starting geometry or as the optimized geometry?
as highlighted in the documentation:
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
Is it possible to create a full precision .trr coordinate file from a .gro
or any other structure file with modified 8-decimal point coordinates?
I think you are misunderstanding the use of the word precision here. In
general, the same configuration will be represented differently in .trr and
.gro formats, with the former being a closer approximation. Accordingly,
one will get a different result for NMA on the endpoint of GROMACS EM as
observed in the .trr file and as observed in the .gro file. The former will
be closer to the stationary point, and so lead to more acceptable estimates
of the normal modes. However, here you want to do NMA on the same
coordinates with two programs, so it is up to you to represent the
coordinates in a way that the two programs can compute on the same
approximation to the coordinates of the stationary point. There's no need
to convert to .trr (or the QM binary format), because all that does is
treat 2.613 as 2.613.
So a command line like this will do the job, right?
grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p ${ligand}.top
-o nm.tpr
Thomas
==
Thomas Evangelidis
PhD student
Biomedical Research Foundation, Academy of Athens
4 Soranou Ephessiou , 115 27 Athens, Greece
email: tev...@bioacademy.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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[gmx-users] A simulation of pure chloroform with AMBER compatible parameters never gives the right density
Dear Users, I am trying to reproduce the results obtained by Fox Kollman on chloroform presented in the following papers but can never achieve the proper density of 1.459 they obtain with their own rigid CHCL3 model. The best I obtain with the parameters presented below is 1.390. I tried with both version 4.5.3 and 4.0.7. Can anyone help me on that ? Thank you Aymeric Naômé The Journal of Physical Chemistry, 1996, 100, 25, 10779-10783 The Journal of Physical Chemistry B, 1998, 102, 41, 8070-8079 The parameters are: qC=-0.345 eps=0.1094 kcal/mol R*=1.908 Ang. qCl=0.012 eps=0.2550 R*=2.000 qH=0.309 eps=0.0157 R*=1.187 C-Cl=1.758 Ang. C-H=1.100 H-C-Cl=107.7° Cl-C-Cl=112.2° And my corresponding topology file is the following: sigma=2*(R*/10)/(2^(1/6)) epsilon=eps*4.184 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 0.5 0.8333 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon CT 6 12.010. A 3.39967e-01 4.57730e-01 H3 1 1.008 0. A 2.11499e-01 6.56888e-02 Cl 17 35.453 0. A 3.56359e-01 1.10669e+00 [ moleculetype ] ; Namenrexcl CHCL3 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 CT 1 CHCL3 C 1 -0.345 12.011 ; qtot -0.386 2 H3 1 CHCL3 H 1 0.309 1.008 ; qtot -0.120 3 Cl 1 CHCL3Cl1 1 0.012 35.453 ; qtot -0.080 4 Cl 1 CHCL3Cl2 1 0.012 35.453 ; qtot -0.040 5 Cl 1 CHCL3Cl3 1 0.012 35.453 ; qtot 0 [ constraints ] 1 3 10.1758 1 4 10.1758 1 5 10.1758 1 2 10.1100 ;2 3 20.2340 2 4 20.2340 2 5 20.2340 3 4 20.2901 4 5 20.2901 5 3 20.2901 [ system ] ; Name CHCl3_256 [ molecules ] ; Compound#mols CHCL3 256 The simulation parameters in the first paper: MD program: AMBER 4.1 200-300 molecules dt=2fs (rigid model) cut-off=12 Ang. long range correction according to AllenTildesley Berendsen thermostat with coupling constant 0.4 ps-1 temperature=300 K inverse compressibility 1.086 10-4 bar-1 Berendsen barostat with coupling constant 0.2 ps-1 pressure=1 atm SHAKE constraint solver Below is my mdp file with the corresponding parameters: title = CHCl3_box cpp = /lib/cpp -traditional define = constraints = integrator = md dt = 0.002; fs ! nsteps = 40 ; total 1 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = cut-off rcoulomb= 1.2 rvdw= 1.2 DispCorr= EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes energygrps = CHCL3 ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 5 tc_grps = CHCL3 ref_t = 300 ; Pressure coupling is on Pcoupl = Berendsen pcoupltype = isotropic tau_p = 2.5 compressibility = 10.86e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ; Energy group exclusion energygrp_excl = freezegrps = freezedim = ; Non-equilibrium Thermodynamics acc_grps= accelarate = ; center of mass comm_mode = linear comm_grps = ; Type of constraint algorithm constraint-algorithm = Shake -- Aymeric Naômé Ph. D. Student UCPTS Division University of Namur 61 Rue de Bruxelles 5000 Namur BELGIUM -- 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] A simulation of pure chloroform with AMBER compatible parameters never gives the right density
On 2011-12-20 15:03, ana...@fundp.ac.be wrote: Dear Users, I am trying to reproduce the results obtained by Fox Kollman on chloroform presented in the following papers but can never achieve the proper density of 1.459 they obtain with their own rigid CHCL3 model. The best I obtain with the parameters presented below is 1.390. I tried with both version 4.5.3 and 4.0.7. Can anyone help me on that ? Thank you Haven't tried that one, but we have OPLS/AA and GAFF, see: http://virtualchemistry.org/molecules/67-66-3/index.php for those the density is too low as well. Aymeric Naômé The Journal of Physical Chemistry, 1996, 100, 25, 10779-10783 The Journal of Physical Chemistry B, 1998, 102, 41, 8070-8079 The parameters are: qC=-0.345 eps=0.1094 kcal/mol R*=1.908 Ang. qCl=0.012 eps=0.2550 R*=2.000 qH=0.309 eps=0.0157 R*=1.187 C-Cl=1.758 Ang. C-H=1.100 H-C-Cl=107.7° Cl-C-Cl=112.2° And my corresponding topology file is the following: sigma=2*(R*/10)/(2^(1/6)) epsilon=eps*4.184 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 0.5 0.8333 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon CT 6 12.01 0. A 3.39967e-01 4.57730e-01 H3 1 1.008 0. A 2.11499e-01 6.56888e-02 Cl 17 35.453 0. A 3.56359e-01 1.10669e+00 [ moleculetype ] ; Name nrexcl CHCL3 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 CT 1 CHCL3 C 1 -0.345 12.011 ; qtot -0.386 2 H3 1 CHCL3 H 1 0.309 1.008 ; qtot -0.120 3 Cl 1 CHCL3 Cl1 1 0.012 35.453 ; qtot -0.080 4 Cl 1 CHCL3 Cl2 1 0.012 35.453 ; qtot -0.040 5 Cl 1 CHCL3 Cl3 1 0.012 35.453 ; qtot 0 [ constraints ] 1 3 1 0.1758 1 4 1 0.1758 1 5 1 0.1758 1 2 1 0.1100 ; 2 3 2 0.2340 2 4 2 0.2340 2 5 2 0.2340 3 4 2 0.2901 4 5 2 0.2901 5 3 2 0.2901 [ system ] ; Name CHCl3_256 [ molecules ] ; Compound #mols CHCL3 256 The simulation parameters in the first paper: MD program: AMBER 4.1 200-300 molecules dt=2fs (rigid model) cut-off=12 Ang. long range correction according to AllenTildesley Berendsen thermostat with coupling constant 0.4 ps-1 temperature=300 K inverse compressibility 1.086 10-4 bar-1 Berendsen barostat with coupling constant 0.2 ps-1 pressure=1 atm SHAKE constraint solver Below is my mdp file with the corresponding parameters: title = CHCl3_box cpp = /lib/cpp -traditional define = constraints = integrator = md dt = 0.002 ; fs ! nsteps = 40 ; total 1 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = cut-off rcoulomb = 1.2 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes energygrps = CHCL3 ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 5 tc_grps = CHCL3 ref_t = 300 ; Pressure coupling is on Pcoupl = Berendsen pcoupltype = isotropic tau_p = 2.5 compressibility = 10.86e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; Energy group exclusion energygrp_excl = freezegrps = freezedim = ; Non-equilibrium Thermodynamics acc_grps = accelarate = ; center of mass comm_mode = linear comm_grps = ; Type of constraint algorithm constraint-algorithm = Shake -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] [Fwd: h-bonds constraints]
---BeginMessage--- Hi I want to run an NPT simulation with all h-bonds constrained. How does grompp identify the Hydrogen atoms given that forcefield labels like HA, HC, HE are used. Is it the mass? Many Thanks Gavin ---End Message--- -- 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] About conformation choice for Umbrella sampling
Dear justin , i regret inconvenience in the previous mail Instead of taking PDB based on g_dist over all frames Can i choose various .gro files for doing umbrella sampling based on the pullf.xvg . file In that file plot of force Vs time is available. i am selecting the PDBs from near maxima of force time profile curve to time of major structural change . in my case Example ( 120ps to 380ps) can i use those PDBs for Umbrella sampling othewise should i not consider time for umbrella sampling? I am expecting your valuable reply Thanks in Advance -- 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] umbrella sampling with replica exchange
Hi, I have a technical question regarding feasibility of combining replica exchange with umbrella sampling or any other pulling simulations in gromacs. Since the umbrella sampling or any other pulling simulations are non-equilibrium simulation due to presence of external bias, I wonder whether the detailed balance in replica exchange simulation will be maintained . I ask this because replica exchange uses Monte Carlo metropolis algorithm to swap configurations and so I wanted to know what is the energy-difference ( New energy - old energy) in metropolis algorithm gromacs will use : Is it the energy difference after taking into account the biasing potential or is is only the internal potential energy-difference ( i.e not including biasing potential ) ? Any response from the users or developer will be highly appreciated. Thanks Sanku-- 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] [Fwd: h-bonds constraints]
Gavin Melaugh wrote: Subject: h-bonds constraints From: Gavin Melaugh gmelaug...@qub.ac.uk Date: Mon, 19 Dec 2011 10:20:40 + To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Hi I want to run an NPT simulation with all h-bonds constrained. How does grompp identify the Hydrogen atoms given that forcefield labels like HA, HC, HE are used. Is it the mass? The atom name designates whether or not it's a hydrogen. See the count_hydrogens routine in topshake.c. -Justin -- 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 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] About conformation choice for Umbrella sampling
vidhya sankar wrote: Dear justin , i regret inconvenience in the previous mail I have no experience with PLUMED; I could not comment. I have been extremely busy lately. Instead of taking PDB based on g_dist over all frames Can i choose various .gro files for doing umbrella sampling based on the pullf.xvg . file In that file plot of force Vs time is available. i am selecting the PDBs from near maxima of force time profile curve to time of major structural change . in my case Example ( 120ps to 380ps) can i use those PDBs for Umbrella sampling othewise should i not consider time for umbrella sampling? I'm sorry, I have no clear idea what you're even trying to accomplish. -Justin -- 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 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] a doubt about pbc nojump or mol or whole
Dear gmx-users, I've just finished several simulations of 4 single point mutants of my dimeric protein in rhombic dodecahedron box (-d 1.5 nm) centered on the protein, filled with water, neutralized with sodium, simulated with Gromacs 4.5.3 for 30 ns after NVT and NPT dynamics. I made simulations in the same way and with the same settings, obtaining 4 trajectories. When I obtained trajectories, I used trjconv to reset the visualization of my systems: trjconv -f traj.xtc -s traj.tpr -pbc mol -ur compact -o traj_mol.xtc (selecting 0=System when prompted) then I used g_mindist to calculate minimum distance between periodic images. The resulting graphs showed me that for all simulations the distance is never lower than 2.0 nm, but for only one system there are some spikes in the final part of the simulation (between 25 and 30 ns) lowering the min distance below 1 nm (only in correspondence of these spikes). I also calculated the rmsd using as reference the .gro file obtained in this way (as suggested sometimes ago by somebody of you, perhaps Justin or Tsjerk): editconf -f traj.tpr -o traj_0ns.gro trjconv -f traj_0ns.gro -s traj.tpr -pbc mol -ur compact -o traj_mol.gro (selecting 0=System when prompted) then: g_rms -f traj_mol.xtc -s traj_mol.gro -o traj_mol_rms.xvg (selecting 4=Backbone when prompted) I see a quite stable rmsd around 0.2 nm for all systems, with spikes up to 4 nm in the same system that showed problems with g_mindist, in positions corresponding to the spikes in the g_mindist.xvg graph. Looking at this trajectory with VMD, I saw that in correspondence with the spikes, the two monomers of the protein dissociate and appear in different parts of the simulation box (i.e. my periodic image is formed by one monomer, and another monomer is seen in correspondence with another periodic image). All the other systems move into the periodic box, without dissociating into monomers. In order to manage this issue, I applied nojump to the trajectory of this anomalous system: trjconv -f traj_mol.xtc -s traj.tpr -pbc nojump -o traj_molnoj.xtc When I repeated the analyses with g_mindist and g_rms, I see graphs perfectly superimposed to the former graphs, except for spikes that have been disappeared. What I would like to know is: - Did I make the correct procedure to treat these systems? - Can I compare the results obtained on this -mol + -noj trajectory with the other trajectories -mol only? - In your opinion, is the dissociation of the two monomers only a problem of visualization (given that this protein behaves apparently normally after applying pbc nojump), or I have to suppose that this system is anomalous only for this fact? Any help would be very appreciated. Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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] a doubt about pbc nojump or mol or whole
Hi Anna, Jumps like that are a consequence of PBC. Nothing wrong. Removing jumps like you did is the proper treatment. Cheers, Tsjerk On Dec 20, 2011 9:27 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: ** Dear gmx-users, I've just finished several simulations of 4 single point mutants of my dimeric protein in rhombic dodecahedron box (-d 1.5 nm) centered on the protein, filled with water, neutralized with sodium, simulated with Gromacs 4.5.3 for 30 ns after NVT and NPT dynamics. I made simulations in the same way and with the same settings, obtaining 4 trajectories. When I obtained trajectories, I used trjconv to reset the visualization of my systems: trjconv -f traj.xtc -s traj.tpr -pbc mol -ur compact -o traj_mol.xtc (selecting 0=System when prompted) then I used g_mindist to calculate minimum distance between periodic images. The resulting graphs showed me that for all simulations the distance is never lower than 2.0 nm, but for only one system there are some spikes in the final part of the simulation (between 25 and 30 ns) lowering the min distance below 1 nm (only in correspondence of these spikes). I also calculated the rmsd using as reference the .gro file obtained in this way (as suggested sometimes ago by somebody of you, perhaps Justin or Tsjerk): editconf -f traj.tpr -o traj_0ns.gro trjconv -f traj_0ns.gro -s traj.tpr -pbc mol -ur compact -o traj_mol.gro (selecting 0=System when prompted) then: g_rms -f traj_mol.xtc -s traj_mol.gro -o traj_mol_rms.xvg (selecting 4=Backbone when prompted) I see a quite stable rmsd around 0.2 nm for all systems, with spikes up to 4 nm in the same system that showed problems with g_mindist, in positions corresponding to the spikes in the g_mindist.xvg graph. Looking at this trajectory with VMD, I saw that in correspondence with the spikes, the two monomers of the protein dissociate and appear in different parts of the simulation box (i.e. my periodic image is formed by one monomer, and another monomer is seen in correspondence with another periodic image). All the other systems move into the periodic box, without dissociating into monomers. In order to manage this issue, I applied nojump to the trajectory of this anomalous system: trjconv -f traj_mol.xtc -s traj.tpr -pbc nojump -o traj_molnoj.xtc When I repeated the analyses with g_mindist and g_rms, I see graphs perfectly superimposed to the former graphs, except for spikes that have been disappeared. What I would like to know is: - Did I make the correct procedure to treat these systems? - Can I compare the results obtained on this -mol + -noj trajectory with the other trajectories -mol only? - In your opinion, is the dissociation of the two monomers only a problem of visualization (given that this protein behaves apparently normally after applying pbc nojump), or I have to suppose that this system is anomalous only for this fact? Any help would be very appreciated. Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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 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] Voronoi tessellation
Thanks a lot , will try that Ramya Parthasarathi ramya.sar...@aol.com -Original Message- From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Dec 16, 2011 11:16 am Subject: Re: [gmx-users] Voronoi tessellation Ramya Parthasarathi wrote: Hi I am working with phospholipid bilayers and I would like to plot the 2D Voronoi Tessellation , can any one tell me how to start about it. Not with any Gromacs tool. But these might be useful: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21973/abstract http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ -Justin -- 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 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 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] pressure profiles
It will be saved in the .edr file. Use g_energy to extract the data you are interested in. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ramya Parthasarathi Sent: Wednesday, 21 December 2011 9:06 AM To: gmx-users@gromacs.org Subject: [gmx-users] pressure profiles Hi, I am simulating DOPC lipid molecules in water, i would like to plot the pressure profiles, for the systems i have . Can someone tell me , is there any option in GROMACS which can give the pressure profile? Ramya Parthasarathi ramya.sar...@aol.com -- 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] Normal Mode Analysis starting from an optimized geometry and known partial charges
On 12/21/2011 12:57 AM, Thomas Evangelidis wrote:
Mark, thanks for the prompt response!
I have done Normal Mode Analysis and have calculated partial
charges and the optimized geometry of a few compounds using
high-level QM calculations. Now I want to see (if possible) how
well GROMACS can reproduce the normal modes if I start from the
same optimized geometry and use the same partial charges.
In general for NMA to make sense you need to be at a stationary
point w.r.t. the atomic degrees of freedom of the model being
used. That won't be quite true at a QM geometry, so there's a
sense of apples-vs-oranges comparison.
If I get it right you mean that NMA in GROMACS must start from an
energy minimum (stationary point) w.r.t the ff used (GAFF in my case),
which means that an energy minimization is neccessary ever if I use an
QM optimum geometry and the respective partial charges. Namely there
is no way to reproduce the normal modes I obtained from QM
calculations, correct?
You can choose to compare the two models on the same configuration, or
at the local minimum w.r.t. each model that is nearest some
configuration. Each approach has a minor flaw. How you need to manage
precision varies with the choice you make.
An obvious problem is that the starting compound geometry is not
in full precision
The starting geometry is in full precision if it's the same as
that used for the QM calculation. That is quite possible to
achieve with .pdb or .gro input.
The same as the starting geometry or as the optimized geometry?
Your choice - your original workflow did no EM in GROMACS, so the use of
.trr format was immaterial.
as highlighted in the documentation:
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
Is it possible to create a full precision .trr coordinate file
from a .gro or any other structure file with modified 8-decimal
point coordinates?
I think you are misunderstanding the use of the word precision
here. In general, the same configuration will be represented
differently in .trr and .gro formats, with the former being a
closer approximation. Accordingly, one will get a different result
for NMA on the endpoint of GROMACS EM as observed in the .trr file
and as observed in the .gro file. The former will be closer to the
stationary point, and so lead to more acceptable estimates of the
normal modes. However, here you want to do NMA on the same
coordinates with two programs, so it is up to you to represent the
coordinates in a way that the two programs can compute on the same
approximation to the coordinates of the stationary point. There's
no need to convert to .trr (or the QM binary format), because all
that does is treat 2.613 as 2.613.
So a command line like this will do the job, right?
grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p
${ligand}.top -o nm.tpr
That copies the configuration in -c in the full precision available from
the format of -c into the .tpr.
Mark
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[gmx-users] CTAB force field
Dear all, I prepare to do simulation about the solution of CTAB. Does anyone know the force field (top and gro files) of CTAB which were published before? Thank you very much. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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] Possible typo in nb_kernel_x86_64_sse.c (4.5.5)
Hi, this is on purpose. Since 4.5 GROMACS requires SSE2. It is used for e.g. the GB kernels. Because CPUs with SSE1 support but no SSE2 are so old we don't try to support them anymore even for those kernels not requiring SSE2. Roland On Tue, Dec 20, 2011 at 6:05 AM, Daniel Adriano Silva M dadri...@gmail.comwrote: Hi Devs, Is this intended or just a typo: #nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.c# .: 211:fprintf(log,Testing x86_64 SSE2 support...); .: ## instead of: .: 211:fprintf(log,Testing x86_64 SSE1 support...); .: The same thing appears in other _sse.c files. Thanks, Daniel -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] maxh not causing termination
On 12/19/2011 1:51 PM, Ben Reynwar wrote: I'm having a problem with gromacs not terminating as expected when using the maxh option. It is an REMD simulation with 32 replicas. I'm specifying -maxh 24 and as expected see the following in the stderr output. Step 773882: Run time exceeded 23.760 hours, will terminate the run Step 773876: Run time exceeded 23.760 hours, will terminate the run Step 773880: Run time exceeded 23.760 hours, will terminate the run etc However I can see that the output files continued to be written for another hour until at 25 hours the simulation was terminated by the queueing system. No checkpoint files were produced. The output files show that the simulation continued until about step 797000. I've done similar things previously without running into this problem. Anyone have any ideas for what stupid mistake I could be making? Perhaps none. What GROMACS version is this? Does the latest version have the same behaviour? Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] Possible typo in nb_kernel_x86_64_sse.c (4.5.5)
Got it. Thanks. Daniel On Dec 21, 2011 9:46 AM, Roland Schulz rol...@utk.edu wrote: Hi, this is on purpose. Since 4.5 GROMACS requires SSE2. It is used for e.g. the GB kernels. Because CPUs with SSE1 support but no SSE2 are so old we don't try to support them anymore even for those kernels not requiring SSE2. Roland On Tue, Dec 20, 2011 at 6:05 AM, Daniel Adriano Silva M dadri...@gmail.com wrote: Hi Devs, Is this intended or just a typo: #nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.c# .: 211:fprintf(log,Testing x86_64 SSE2 support...); .: ## instead of: .: 211:fprintf(log,Testing x86_64 SSE1 support...); .: The same thing appears in other _sse.c files. Thanks, Daniel -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 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] regarding rtp file
hello sir, Thanks for your reply.. As you suggest i tried with all available forcefield for my lipopeptide but i am getting the same error,, *Processing chain 2 'A' (16 atoms, 1 residues) Warning: Starting residue BFC1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'BFC' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ---* since mine is connected cyclic lipopeptide even i cant try using prodrg server too. i dono how to generate my topology file. pls help me with your answer. Thanking you, -- 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] regarding rtp file
priya thiyagarajan wrote: hello sir, Thanks for your reply.. As you suggest i tried with all available forcefield for my lipopeptide but i am getting the same error,, I have posted this link several times before: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field All the necessary steps are spelled out there. There is no force field that will contain the residue you seek; you have to add it yourself. *Processing chain 2 'A' (16 atoms, 1 residues) Warning: Starting residue BFC1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. The error message tells you exactly what is wrong (in this case, not completing step #5 in the link above). 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: Residue 'BFC' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ---* http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database Also, a result of not completing step #1 in the adding a residue link above. since mine is connected cyclic lipopeptide even i cant try using prodrg server too. i dono how to generate my topology file. pls help me with your answer. I've tried and at this point am repeating myself. Also note that there are numerous posts in the list archive about dealing with cyclic peptides (which are not trivial). I would suggest you search for them. You should also simplify your system until you understand the workflow. Deal with a custom residue in a normal linear peptide, then introduce the cyclic peptide and the issues it may present. -Justin -- 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 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
As suggested by David I extended the simulations (total of 25ns) for a single chain polyacid in 5500 water molecules and tried to calculate the H-bond ACF. I get the same negative lifetime for Hbonds between COOH groups and water. Is it that the g_hbond ACF giving weird results for this case. For chains with COO- and COOH groups (50% each), I got positive life times of Hbond. Ayy ideas on how to solve this will be of great help. I am using 4.0.7 version. The command line I gave was g_hbond -f traj.xtc -s traj.tpr -n index.ndx -ac and chose the polyacid and the water as the two groups. ACF 22057/22057 Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0146697 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward-0.271 -3.687-666.000 0.0146697 Backward -2.291 -0.437-666.000 One-way 0.101 9.882 10.207 Integral0.034 29.376 12.907 Relaxation 0.063 15.803 11.370 Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India On Tue, Dec 13, 2011 at 10:12 AM, sulatha M. S mssula...@gmail.com wrote: I did not get a warning here. I also have simulations (20ns) of copolyacids where again it gave me negative life time. These runs are well equilibrated with respect to energy and Rg of the polymers. The system is a 20 repeat unit chain in approx. 5500 water molecules. I have done simulations in which 10 units are COO- and the remaining 10 as COOH along the chain. With a 10ns trajectory, the average life time of H-bonds is positive.Only in the case of unionized acid I am getting a negative life time. Did you look at the ACF graph? It could be constant at 1 or 0. Yes, the ACF decays to 0 and remains constant in all cases Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists What is the value for free energy of H-bonding. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 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:Getting energy values in kcal/mol
Hi, I am running MD simulation for my system using Gromacs , as the output energies values generated are in the units of kJ/mol , Is there any option or method while running the simulation which i can use so that i get output energies in the units of kcal/mol rather than in kJ/mol.I have gone through the gromacs manual and mailing list but could not find the solution. Any help will be highly appreciated. Rajitha Ph.D student -- 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] Re:Getting energy values in kcal/mol
On 12/21/2011 5:44 PM, Sairam Tatikonda wrote: Hi, I am running MD simulation for my system using Gromacs , as the output energies values generated are in the units of kJ/mol , Is there any option or method while running the simulation which i can use so that i get output energies in the units of kcal/mol rather than in kJ/mol.I have gone through the gromacs manual and mailing list but could not find the solution. Any help will be highly appreciated. No. You will need to convert these yourself if you need it. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] regarding itp
hello sir, thanks for your reply.. sorry for disturbing you again and again.. i understood that i need to add my residue BFC in my rtp file and residuetype.dat file. i like to clarify one thing. i added BFC as lipid in my residuetypes.dat file. then i need to include my residue BFC in .rtp file. To add in that rtp file i need itp file for my fattyacid. so that can use those atomtypes dihedrals in my rtp. am i correct.. -- 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] regarding itp
On 12/21/2011 5:53 PM, priya thiyagarajan wrote: hello sir, thanks for your reply.. sorry for disturbing you again and again.. i understood that i need to add my residue BFC in my rtp file and residuetype.dat file. i like to clarify one thing. i added BFC as lipid in my residuetypes.dat file. then i need to include my residue BFC in .rtp file. To add in that rtp file i need itp file for my fattyacid. so that can use those atomtypes dihedrals in my rtp. am i correct.. pdb2gmx uses the .rtp entries to construct a [moleculetype], as you already know from your reading of chapter 5 (particularly section 5.6) of the manual... right? A molecule .itp file already contains a [moleculetype]. Both of those need to either declare their function parameters on the line that uses them, or rely on grompp to later look them up from the atom types in the force field .itp files. So you need either to map the atoms in your BFC to the pre-defined atomtypes so that the existing parameters can be looked up, or you need to develop the parameters yourself (which would be a bad idea at what appears to be your current level of experience). Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] restraint force and free enrgy code.
Dear Everyone: I need to calculate the free energy change of restraining the ligand in the binding site. I wonder if or not the restraint force can be directly controlled by the free energy code, which means by different lambda values. I checked the manual of gromacs 4.5.4 but can not found any clue for that. But I do think someone mentioned that it can be done in some version of gromacs. Does anyone can tell me if it is true? Thanks a lot! -- Best regards, Hanzi Sun@HuangLab NIBS -- 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
