[gmx-users] ensemble selection
Dear Justin I'm simulating gold nanoparticle interaction with protein by OPLSAA forcefield. I'm confused for selection an ensemble for my md run. I did energy minimization by NPT . then I did the MD by NVT. I did it because of studying of two paper that were similar to my project (Adsorption of histidine and histidine-containing peptides on Au(1 1 1):A molecular dynamics study by Zhen Xu, Shi-Ling Yuan and Interaction of b-Sheet Folds with a Gold Surface by Martin Hoefling, Susanna Monti, Stefano Corni). But in manual and tutorials of gromacs is proposed energy minimization should be done by NVT and NPT and then MD should be done with NPT ensemble. in your idea should I repeat my MD run by NPT ensemble? what is the difference of my result between this two? thank you Fatemeh Ramezani -- 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] protein unfolding in water
dear users I'm studying gold nano-particle effect on one of the blood protein stability and structure. one time I simulated the protein in the presence of the gold nanoparticle and once without nanoparticles. when I simulated protein alone in water, I expected the protein to remain stable but protein RMSD, gyration,dssp and graphs show protein structure is changing and protein helices are opening during the simulation. Thus, I can not study nanoparticle interaction effect on the protein structural changes , because the structural changes also observed in the absence of nanoparticle. I think there is a problem. What is the solution you offer me? What is the problem? sincerely Fatemeh Ramezani -- 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] forcefield and setting
Dear Justin I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for water. em.mdp file: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 4 constraint_algorithm = shake_tol = 0.0001 nstenergy = 10 nstxtcout = 1 nstlist = 5 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 8 ewald_rtol = 1e-5 optimize_fft = yes emtol = 1000.0 emstep = 0.01 md.mdp file: title = n.pdb restraining cpp = /lib/cpp constraints = none integrator = md dt = 0.0008 nsteps = 2500 nstcomm = 10 comm_mode = nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rcoulomb-switch = 1 rvdw = 0.5 vdwtype = shift ;rvdw-switch = 0.6 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in three groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Protein Non-Protein ref_t = 300 300 ; Pressure coupling is on ;Pcoupl = berendsen Pcoupl = no Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 energygrps = Protein Sol Fatemeh Ramezani -- 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] aminoacids protonation in different ph
Dear Justin I found a server : http://biophysics.cs.vt.edu/ that protonate aminoacids according to desired pH easily. Sincerely Fatemeh Ramezani -- 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] AMINOACIDS
Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? Thank you Fatemeh Ramezani -- 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
Fw: [gmx-users] AMINOACIDS
Dear Justin I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid deprotonate? and if pKa of aminoacids is bigger thanmy desired pH, I must protonate this amino acid? Thank you Fatemeh Ramezani - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 15 July 2013, 17:00 Subject: Re: [gmx-users] AMINOACIDS On 7/15/13 7:56 AM, fatemeh ramezani wrote: Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? There are various methods for pKa calculations, and based on those results you can choose the appropriate states with pdb2gmx command-line options. Again, this topic is covered extensively in the archive and you would benefit from some of the previous discussions that I will not repeat here. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] acidic pH
Hello dear users I'm simulating gold nanoparticle interaction with protein. I want to change the pH of system. What would need to be changed to simulate this system at pH 3.0? thanks you Fatemeh Ramezani -- 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] fattyn acid parameter in OPLSAA forcefield
Hi all I want to simulate protein-fatty acid-AU complexs by OPLSAA force field. But OPLSAA force field, hasn't any parameter for fatty acid. Can I use CHARMM fatty acid parameters in OPLSAA force field? Anyone has better suggestion? Fatemeh Ramezani -- 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] interaction energy
HI I'm simulating gold-protein interaction by gromacs. after MD simulation I want to calculate interaction energy of each aminoacids with AU surface. Enon-bond = E(vdw) + E(elec) gold atoms charge in simulation were considered 0, then E non-bonded=E(vdw) Is this true? The interaction energy is equal to the van der Waals energy? Fatemeh Ramezani -- 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:Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology
Dear Justin I thought by use of -pairs I can calculate energy between any 2 groups from index file. when I use g_energy, result is a .xvg file that shows energy of system but I need to calculate energy between specific groups. is there any way for me? thanks Fatemeh Ramezani -- 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] binding energy calculation when appear this error: no distance restraints in topology
the command that I used is : g_energy -f md300.edr -s fws_md300.tpr -o energy.xvg -pairs pairs.xvg Fatemeh Ramezani From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 14 April 2013, 21:15 Subject: Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology On 4/14/13 9:38 AM, fatemeh ramezani wrote: Dear all After simulation of gold-protein interaction, now I want to calculate binding energy of each residue to gold. but when I use g_energy command appear this error: No distance restraints in topology How can I calculate binding energy without running simulation again(because it takes about one week and I need this result as soon as possible) ? Please provide the exact command you used. There is no reason for g_energy to be reading a topology to extract this information. You can get so-called nonbonded interaction energies decomposed by energy group, but whether or not you can call this an actual binding energy is highly questionable. -Justin -- 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] can I change atom position after x steps
Dear all I am simulating gold nanoparticle interaction with 10 aminoacids.Two amino acids have been far from the nanoparticleafter 2000 steps. Now, Can I change after2000 steps, the position of these 2 aminoacids in PDP file and then continue the simulation? Fatemeh Ramezani -- 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] bonding energy
I would check the energy connection between an amino acid and a ligand. After simulation, I run the following command: g_dist_mpi -f x.trr -s x.tpr -n index.ndx -o pro.xvg Then I choose the bond option (option 1) from the proposed options. Is this true for energy bonding finding between two molecules? thank you Fatemeh Ramezani -- 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] au-protein separate minimization
Dr. Justin I want to do energy minimization of AU and Protein in separate steps and in last emails you said a way for this, is freezing of them. Then I decide to freeze AU and minimize Protein and in next step vise versa. I'm wrong? Fatemeh Ramezani -- 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] au-protein simulation, water constraint_algorithm
Dr. Justin In GOLP paper is written: Water molecules were kept rigid with the SETTLE algorithm, but in its commented md.mdp file is written define = ;GOLP has been tested with lincs only constraint = none constraint_algorithm = lincs according to manual, SETTLE can be selected in the topology, means that with the above settings in md.mdp file, should I add [ settles ] ; OW funct doh dhh 1 1 0.1 0.16333 in .top file? Are these settings correct? If that is the constraint = none, constraint_algorithm = lincs applies? many thanks Fatemeh Ramezani -- 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] separate equilibrium
hi I'm simulating gold nanoparticle interaction with amino acids. I would like first equilibrate the nanoparticle and freeze it. Then I equilibrate protein .Meaning that I want equilibrate them separatelywhile both of them are in one box full of water. And after equilibrium phase I start simulation of them. How can I do this? Fatemeh Ramezani -- 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] au--protein separate equilibration
1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein SOL freezedim = Y Y Y Y Y Y comm_mode = None 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None 3. In simulation, I'm using this md.mdp file: title = Yo cpp = /lib/cpp define = integrator = md tinit = 0.0 dt = 0.002 nsteps = 25 nstxout = 2500 nstvout = 2500 nstlog = 500 nstenergy = 250 nstxtcout = 0 pbc = xyz rlist = 1.00 coulombtype = PME r_coulomb = 1.00 fourierspacing = 0.10 pme_order = 6 ewald_rtol = 1e-6 vdw-type = switch rvdw-switch = 0.90 rvdw = 1.00 tcoupl = nose-hoover tc_grps = SOL AUS AUB AUI tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 Pcoupl = no gen_vel = yes gen_temp = 10 gen_seed = 173529 ; GolP has been tested with lincs only constraints = none constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 lincs_warnangle = 80 freezegrps = AU AUI freezedim = Y Y Y Y Y Y comm_mode = None Are these .mdp file right? Fatemeh Ramezani -- 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
Fw: [gmx-users] au--protein separate equilibration
Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that I freeze AU atoms in it, minimization would be true? title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein freezedim = Y Y Y comm_mode = None 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None -- 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: gold-protein simulation
Dear Justin What you said is true for bonded parameters, but how about the parameters of the nonbonded file? Why Despite any non-bonded parameters (Sigma, Epsilon) are considered between the gold atom and the other atoms , protein is stretched to the gold cluster ? What is the reason for this closing?Is not it true that when there is no epsilon and Sygma between two atoms, should not be move toward one another? Fatemeh Ramezani -- 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] (no subject)
I didn't set epsilon and sigma between au and other atoms equal to zero, but I have not enteredanyEpsilon and Sigmafor them , and once again I set them zero and try it again. But if closing of gold to protein, is because of charge, how do I delete its effect ? How can I uncharged the system? (Of course, the whole system charge that is shown in the first grompp step is very low near -0.11). Fatemeh Ramezani -- 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 104, Issue 83
Dear Justin I want exactly this, that the distance between Au-S be stable around equilibrium value, For this purpose,Should I put the harmonic parameters related to the gold and sulfur in ffbonded file? Or I should consider AU-S connection as VonderWaals and put its epsilon and sidma in ffnonbonded file? thank you Fatemeh Ramezani From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Tuesday, 18 December 2012, 14:30 Subject: gmx-users Digest, Vol 104, Issue 83 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. merge .gro, .top files (Kieu Thu Nguyen) 2. Re: GPU running problem with GMX-4.6 beta2 (Albert) 3. Re: merge .gro, .top files (Tsjerk Wassenaar) 4. Re: merge .gro, .top files (Erik Marklund) 5. Re: merge .gro, .top files (Vedat Durmaz) 6. Re: Re: gold-S simulation (francesco oteri) -- Message: 1 Date: Tue, 18 Dec 2012 12:18:38 +0700 From: Kieu Thu Nguyen kieuthu2...@gmail.com Subject: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CACrJSRgRHUbjqW+Zpfq=yfmcuh9ow68d2kmvklghez3acas...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- Message: 2 Date: Tue, 18 Dec 2012 09:20:05 +0100 From: Albert mailmd2...@gmail.com Subject: Re: [gmx-users] GPU running problem with GMX-4.6 beta2 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50d02735.9030...@gmail.com Content-Type: text/plain; charset=UTF-8; format=flowed On 12/17/2012 08:06 PM, Justin Lemkul wrote: It seems to me that the system is simply crashing like any other that becomes unstable. Does the simulation run at all on plain CPU? -Justin Thank you very much Justin, it's really helpful. I've checked that the structure after minization and found that there is some problem with my ligand. I regenerated the ligand toplogy with acpype, and resubmit for mimization and NVT. Now it goes well. So probably the problems comes from the incorrect ligand topolgy which make the system very unstable. best Albert -- Message: 3 Date: Tue, 18 Dec 2012 09:30:04 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cabze1siujhgv4o8ndjfsnu4pxtketqmhxdi2i77vhp60nnj...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi KT, If you mean concatenating frames in .gro files, you can use trjcat or just cat. If you mean merging the coordinates, it's a wee bit more complicated. Since you also ask for top files, I guess that's the case. Here's a snippet of python code that will do the trick: #!/usr/bin/env python import sys f = [open(i).readlines() for i in sys.argv[1:]] print Merged gro file\n%5d % (sum([len(i) for i in f]) - 3*len(f)) print .join([.join(i[2:-1]) for i in f]), print f[0][-1] For the top files, it is necessary to ensure all the moleculetypes are #included, and that the [ molecules ] listing under [ system ] has the right number and order of the molecules in the merged gro file. There's no tool for that that I know of. Cheers, Tsjerk On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- Message: 4 Date: Tue, 18 Dec 2012 09:38:41 +0100 From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: bd5228d7-229f-4e9c-9f03-66836dd50...@xray.bmc.uu.se Content-Type: text/plain; charset=us-ascii 18 dec 2012 kl. 09.30 skrev
[gmx-users] Re: gmx-users Digest, Vol 104, Issue 73
Dear Justin According to papers, I expect gold atom interacts with the sulfur atom of amino acid cysteine covalently. But in last email you said in the case of protein-Au This will not be true to add these parameters in topology file. Then in which file should I add the parameters between gold and sulfur? What do you suggest? How do I define for the program that can be established between these two atoms covalent bond ? many thanks Fatemeh Ramezani From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Monday, 17 December 2012, 1:47 Subject: gmx-users Digest, Vol 104, Issue 73 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Parametrisation of the cyclic nucleotides in Gromos force fields (James Starlight) 2. Re: Parametrisation of the cyclic nucleotides in Gromos force fields (Justin Lemkul) 3. Re: gold-S simulation (fatemeh ramezani) 4. Re: gold-S simulation (fatemeh ramezani) 5. Re: gold-S simulation (francesco oteri) 6. Box Pressure on individual box walls (John Doe) 7. Re: Box Pressure on individual box walls (David van der Spoel) 8. Re: gold-S simulation (Justin Lemkul) -- Message: 1 Date: Sun, 16 Dec 2012 19:34:57 +0400 From: James Starlight jmsstarli...@gmail.com Subject: Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAALQopzp6xCweeYWRcmMsZNYDnEvg_=gjpqofrlazphv5dd...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Justin, thanks again for explanation. So the first 5 atoms in cmap.it correspond to the starting sequence of the backbone atoms of the amino acid doesnt it ? So what is the 24 24 numbers at the end of each cmap line ? E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would be assigned as the backbone. That lines were added after grompp produce error about unknown cmap for that 5 atoms of the chromophore. Should the 24 24 \ be removed from each line of the chromophore cmap ? James -- Message: 2 Date: Sun, 16 Dec 2012 11:12:35 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50cdf2f3.4030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 12/16/12 10:34 AM, James Starlight wrote: Justin, thanks again for explanation. So the first 5 atoms in cmap.it correspond to the starting sequence of the backbone atoms of the amino acid doesnt it ? So what is the 24 24 numbers at the end of each cmap line ? Probably something related to how Gromacs tools read in the CMAP data. I don't have time to go through the code to find exactly how it's used. E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would be assigned as the backbone. That lines were added after grompp produce error about unknown cmap for that 5 atoms of the chromophore. Should the 24 24 \ be removed from each line of the chromophore cmap ? You shouldn't be modifying anything about cmap.itp, nor should those numbers be present in your .rtp file. Your [cmap] directive in the .rtp entry should contain a sequence of 5 atom names to which the CMAP corrections are applied. -Justin -- 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 -- Message: 3 Date: Sun, 16 Dec 2012 09:58:16 -0800 (PST) From: fatemeh ramezani fr_...@yahoo.com Subject: Re: [gmx-users] gold-S simulation To: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org, gmx-users@gromacs.org gmx-users@gromacs.org, gmx-users-ow...@gromacs.org gmx-users-ow...@gromacs.org Message-ID: 1355680696.17757.yahoomail...@web113504.mail.gq1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear francesco I extract gold parameter from papers that I attached them for you. But for gold and other atom parameters, you should calculate them using common combination rule. Fatemeh Ramezani -- Message: 4 Date: Sun, 16
Re: [gmx-users] gold-S simulation
Dear francesco I extract gold parameter from papers that I attached them for you. But for gold and other atom parameters, you should calculate them using common combination rule. Fatemeh Ramezani -- 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] gold-S simulation
hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you. Fatemeh Ramezani -- 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] gold-S simulation
hi I'm simulating gold atom interaction with aminoacidcys. I have made gold-cys.pdb by hyperchem software: HETATM 1 N CYS 1 0.000 1.335 0.000 HETATM 2 CA CYS 1 -0.683 1.818 -1.183 HETATM 3 C CYS 1 -0.705 3.339 -1.221 HETATM 4 O CYS 1 -0.184 3.993 -0.319 HETATM 5 CB CYS 1 -2.127 1.330 -1.221 HETATM 6 SG CYS 1 -3.106 1.859 -2.649 HETATM 8 AU AU 8 -2.833 0.428 -1.793 HETATM 9 AU AU 9 -2.647 0.381 -2.869 HETATM 10 AU AU 10 -1.691 1.360 -3.093 HETATM 11 AU AU 11 -0.647 2.706 -2.135 HETATM 12 AU AU 12 -2.742 0.834 -0.456 HETATM 13 AU AU 13 -1.691 2.061 -0.043 HETATM 14 AU AU 14 -0.783 3.136 0.376 HETATM 15 AU AU 15 0.095 3.750 -1.068 HETATM 16 AU AU 16 -2.929 2.480 -2.204 HETATM 17 AU AU 17 -3.285 1.594 -3.328 HETATM 18 AU AU 18 -2.544 2.593 -3.763 HETATM 19 AU AU 19 -1.951 1.260 -2.303 CONECT 1 2 CONECT 0 1 CONECT 2 1 3 5 CONECT 0 2 CONECT 3 2 4 CONECT 4 3 CONECT 5 2 6 CONECT 0 5 CONECT 0 5 CONECT 6 5 CONECT 0 6 CONECT 0 6 CONECT 0 6 END I started simulation by this pdb file. I'm using OPLSAA force field and also I added gold parameter in ffnonbonded.itp : . . . ; Added by DvdS 05/2005 copied from GROMACS force field. SI SI 14 28.08000 0.000 A 3.38550e-01 2.44704e+00 AU AU 79 196.9700 0.000 A 0.29510e+00 22.1120e+00 [ nonbond_params ] AU AU 1 0.0e+00 0.0e+00 ; SC 08/2007: Special Au-N vdw to simulate chemical bond between gold-imidazole AU opls_511 1 3.07000e-01 3.96000e+00 ; SC 05/2008: special Au-C and Au-H to simulate pi-systems alkenes+benzene (and PHE) AU opls_142 1 3.21000e-1 2.65400e+00 AU opls_143 1 3.21000e-1 2.65400e+00 AU opls_144 1 2.67000e-1 1.66500e+00 AU opls_145 1 3.2e-1 2.54600e+00 AU opls_146 1 2.67000e-1 1.66500e+00 AU opls_150 1 3.21000e-1 2.65400e+00 ; +imidazole and His AU opls_506 1 3.21000e-1 2.54000e+00 AU opls_507 1 3.21000e-1 2.54000e+00 AU opls_508 1 3.21000e-1 2.54000e+00 ; +HisH AU opls_509 1 3.21000e-1 2.54000e+00 AU opls_510 1 3.21000e-1 2.54000e+00 ; +TYR AU opls_166 1 3.21000e-1 2.54000e+00 ; +TRP AU opls_500 1 3.21000e-1 2.54000e+00 AU opls_514 1 3.21000e-1 2.54000e+00 AU opls_501 1 3.21000e-1 2.54000e+00 AU opls_502 1 3.55000e-1 3.55000e+00 and I concidered AU-S as bonding connection and I added its parameter (bond stretch, dihedral and angle ) in ffbonded.itp file: [ bondtypes ] ; i j func b0 kb . . . AU SH 1 0.24000 165528.0 ; AU S 1 0.24000 165528.0 ; AU SG 1 0.24000 165528.0 ; . . . [ angletypes ] ; i j k func th0 cth . . . AU SG CB 1 109.00 46.34 AU SH CB 1 109.00 46.34 AU S CB 1 109.00 46.34 . . . [ dihedraltypes ] . . . #define improper_AU_S_CB_CA -180.0 1.2958 2 #define improper_AU_SH_CB_CA -180.0 1.2958 2 #define improper_AU_SG_CB_CA -180 1.2958 2 #define improper_AU_S_C_C 19 0.9196 2 #define improper_AU_SH_C_C 19 0.9196 2 #define improper_AU_SG_C_C 19 0.9196 2 . . . when I run my simulation I dont see any interaction or affinity between gold atom and S atom of cystein, while it is clear that gold shoud has interaction with sulfur. what is its reason? I'm completely confused. I tried anythings that I can but my system doesn't work. please help me Fatemeh Ramezani -- 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] gold-protein simulation stop by error in equilibrum step
hello I want to simulate gold nanoparticles with proteins. I've made a PDF file containing the nanoparticles and proteins, using Hayprkm software.then Ihave used thisPDF fileto start the simulation by gromacs. But in the early stage of equilibrium, I am faced with the following error. application called MPI_Abort(MPI_COMM_WORLD, -1) - procesee 17application called MPI_Abort (MPI_COMM_WORLD, -1) - process Source code file:pme.c, line:538 Fatal error: 2 particles communicated to PME node 17 are more than 2/3 times the cut-off out of the domain decomposition cell of the This usually means that your system is not well equilibrated. I've read previous questions and it is said that the system is unstable, but how do I equilibrium the system? I'm having this trouble in equilibrium step Before beginning of MD. I equilibrate my system in 5 steps. by 5 em.mdp file that I named them em1.mdp, em2.mdp,em3.mdp, md100.mdp(temperature=100 k),md200.mdp(temperature=200k) and after these steps I do main simulation in 300k. I attached all mdp file. in md100.mdp steps, mdrun stops in middle of running and appear above error. please help me to resolve my problem thank you Fatemeh Ramezani-- 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] AU-S bonded parameter
hello I want add Au-S parameter for E(bond)=K*(r-r0)^2 to bonded parameters of OPLSAA forcefield. according to the paper, r0=2.4 A , k(au-s)=4180 [kJ/(mol/Å2)]. But in Gromacs manual K unit is KJ/mol. I dont understand it. for use of k(au-s), should I unitless it or not? meaning, I should multiple this K to sigma(au-s) and then put in bonded file? thank you Fatemeh Ramezani -- 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] au virtual atom
Thanks for your response, but I've read the manual. What I realized is that, for example, I should consider for every two, three or … atoms, a virtual atom. Here are some questions: 1 - Does not important consider which atoms together? or How much is the angle between atoms? 2 -Does I need to manually sort atoms and consider for every group a virtual site? thanks ramezani Fatemeh Ramezani -- 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] au virtual site
Dear gromacs users I want to simulate gold nanoparticle by golp force field that needs to determine virtual sites for Au atoms. I read gromacs manual section 5.2.2 and 4.7 but it is not clear that how can I do it and .also I read virtual site tutorial for CO2 but it is for a 3 atomic molecule and I have a crystal by many atoms. I have a pdb file of my nanoparticle contain 600 atoms. How can specify their virtual site? Should I do it by hand? Do you know any command or software that can help me? ramezani -- 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] DANGLING BOND IN GOLD-PROTEIN SIMULATION
HELLO I want simulate gold-protein complex by Golp forcefield. but when I use pdb_gmx I came across this error There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. PLEASE HELP ME regards, Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
