[gmx-users] Umbrella Sampling tutorial

Dear Justin Very thanks for your reply. > What you described earlier should not be attempted with "distance" > geometry. It won't work very well. The use of restraints is almost > NEVER necessary, especially in the case where the reference group > is much more massive than the pulling group. I w

[gmx-users] Umbrella Sampling tutorial

Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pull_geometry = distance, so, I should fix referen

[gmx-users] Umbrella Sampling tutorial

Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector along which the pulling is being conducted is Z. 1

[gmx-users] Umbrella Sampling tutorial

Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: reference group for pulling. Chain_A: group to which pu

[gmx-users] pbc problem

Dear Mark Very thanks for your reply > To make this clear, center the trajectory on the water and watch the > time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in othe

[gmx-users] pbc problem

Dear Tsjerk Wassenaar Very very thanks for your reply. I used trjconv -pbc mol. pbc problem was solved only for lipid molecules. When I see new trajectory by vmd, there are some problesm about drug molecule. https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx If I show my system as 4 regi

[gmx-users] pbc problem

Dear Justin I attached images related to before (em2.gro) and after equilibration. https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/

[gmx-users] pbc problem

Dear Justin Please check this trajectory file (1.xtc) being smaller than 0.xtc. https://www.dropbox.com/s/9qd2l37qyfqvpox/1.xtc -- 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/Ma

[gmx-users] pbc problem

Dear Justin I want to study translocation of drug molecule in lipid bilayer. My gro file after minimization is em2.gro. After NPT-MD simulation, I obtained npt.gro and 0.xtc files. When I see trajectory by vmd, there are some things abnormal. I guess there is pbc problem. I attached these 3 f

[gmx-users] pbc problem

Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters regi

[gmx-users] pbc problem

Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected all lipid atoms for centering. With my manner, pbc problem was solved just for lip

[gmx-users] pbc problem

Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with fo

[gmx-users] change of bilayer structure during NVT equilibration

Dear Justin Very thanks for your quick reply. > Depends on how you prepared the system. For initial structure of system, I used coordination from website: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html > Probably there were voids in the solvent or lipid headgroups that caused > distor

[gmx-users] change of bilayer structure during NVT equilibration

Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER in a rectangular box. I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what

[gmx-users] Re: grompp for minimization: note & warning

Dear Mark > The UNIX tool diff is your friend for comparing files. Thanks for your suggestion. I used diff and sdiff toll for comparing 2 files (before and after correction). diff old.gro new.gro These tolls did not give me any output file or text containing difference between 2 files. In this

[gmx-users] Re: grompp for minimization: note & warning

Dear Tsjerk Thanks for your reply Before correcting the gro file, I knew that gro file is fixed format. I did this correction very carefully. Part of the gro file before and after correction is as follows: - before: ---

[gmx-users] Re: grompp for minimization: note & warning

Dear Tsjerk Thanks for your consideration. I ignored Warning 1. > WARNING 1 [file topol.top, line 32]: > 3632 non-matching atom names > atom names from topol.top will be used > atom names from system.gro will be ignored Based on your suggestion, I checked non-matching atom names between t

[gmx-users] Re: grompp for minimization: note & warning

Dear Tsjerk Thanks for your consideration. My system contains 2 components: (DOPC & cholesterol) lipids + water molecules. I get force field parameters from lipid book (for dopc and cholesterol). I used input coordinate file (system.gro) from following web site: http://people.su.se/~jjm/Stockh

[gmx-users] grompp for minimization: note & warning

Dear Justin I did minimization with the newest version of gromacs (4.6.3). But, unfortunately, problem was not solved. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.o

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin Very very thanks for your quick reply. I am very confused and amazed. After visualization of atom 618 ( where the maximum force is), what should I do to resolve me problem. Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin Thanks for your time and consideration. > As I suggested before, visualize the output file and figure out what is > around atom 618 to cause such forces. I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc molecule (this dopc molecule is intact and is not broken

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin Thanks for your reply > You're still working with outdated software. Please follow my > suggestion of trying 4.6.3. I try to install 4.6.3. > The larger issue, in the end, is the unphysical configuration of the drug > in the membrane. Independent of Gromacs version, that setup wi

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin I used newer version of gromacs (4.6.1), but my problem was not solved. Any help will highly appreciated. -- 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_Lis

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin Very very thanks for your quick reply. > The sys.gro file is positioned within a box that is too large, a fact that is > easily observable in VMD. I suspect that the void space results in > instability. If I positioned system in a smaller box, my problem (instability) solved ???

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin Very very thanks for your quick reply. > The sys.gro file is positioned within a box that is too large, a fact that is > easily observable in VMD. I suspect that the void space results in > instability. If I positioned system in a smaller box, my problem (instability) solved ???

[gmx-users] grompp for minimization: note & warning

Dear Justin About following warning in grompp using WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) You said "You probably have molecules split across PBC in the input coordinate file. here's nothing wrong in that case" I mention

[gmx-users] grompp for minimization: note & warning

Dear Justin Very thanks for your reply. You said "I suspect your Gromacs version is somewhat outdated, as recent versions account for periodicity when making this check". I used 4.5.5 version of gromacs. What version of gromacs is more appropriate for my case. Based on your suggestion, I used -m

[gmx-users] grompp for minimization: note & warning

Dear gromacs users I used -maxwarn option, but after using this command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log I encountered with: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 6.61528 nm Change the

[gmx-users] grompp for minimization: note & warning

Dear gromacs users Nember of groups in each of charge groups is less than or equal 3. charge groups in my itp files are as follows: DOPC.itp: [ atoms ] ; nr type resnr residue atom cgnr char

[gmx-users] grompp for minimization: note & warning

Dear gromacs users My system contains 3 components: DOPC & cholesterol lipids + drug + water molecules. In minimization step, when I use grompp -f em.mdp -c system.gro -p topol.top -o em.tpr, I encountered with following note and warning: WARNING 1 [file em.mdp]: The sum of the two largest charg

[gmx-users] gromos force field in PRODRG server

Dear gromacs users I want to do MD simualation for a protein-ligand system. For ligand, I use PRODRG server. I know that this server generate a *.itp file for ligand based on gromos force field. There are 5 versions for gromos force field (GROMOS96 43a1, GROMOS96 43a2, GROMOS96 45a3, GROMOS96 5

[gmx-users] difference between restrained and constrained

Dear gromacs users I want to know what is difference between restrained EM and restrained EM or between constrained MD and constrained MD. any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the ar

[gmx-users] radius of gyration - compactness - accessible surface area

Dear Tsjerk very thanks for your useful guidance. I now know that I should compare output of g_gyrate (containing Rg vs time) by area.xvg output file of g_sas (containing area vs time). In area.xvg output file, there are several columns: "Hydrophobic", "Hydrophilic" and "Total". for example in

[gmx-users] radius of gyration - compactness - accessible surface area

Dear Tsjerk thanks for your attention. larger radius of gyration, more surface. and smaller radius of gyration, less surface. I want to obtain solvent accessible surface area using g_sas. g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa. I will obtain three output files containing: area.xvg, resar

[gmx-users] radius of gyration - compactness - accessible surface area

Dear Tsjerk thanks for your attention. larger radius of gyration, more surface. and smaller radius of gyration, less surface. I want to obtain solvent accessible surface area using g_sas. g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa. I will obtain three output files containing: area.xvg, resar

[gmx-users] adius of gyration - compactness

Dear Tsjerk thanks for your reply. in paper 1 : larger radius of gyration, less compact, more surface in paper 2: (smaller radius of gyration; not stated explicitly), more compact, less surface. in paper 3: [Journal of Structural Biology 156 (2006) 537–545] Overall, the GBD appears a little

[gmx-users] radius of gyration - compactness

Dear all I am studying md simulation of free protein and protein-ligand and protein-dna complex. In my simulation systems, the average of radius of gyration in free protein is 2.31 and for protein in complex is 2.58. I know the radius of gyration is measurement of compactness of the protein as s

[gmx-users] standard deviation about rmsd and rmsf values

Dear gromacs users I want to know how to obtain standard deviation about rmsd and rmsf values? any help will highly appreciated. -- 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/Mai

[gmx-users] how to obtain binding energy?

Dear Justin thanks for your time and attention in address http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html in Tutorial 3: Umbrella Sampling, in Step One, you said '' For p

[gmx-users] how to obtain binding energy?

Dear Justin and Mohsen Very thanks for your attention Justin you said PMF is much easier in my case (protein-dna complex). Is there tutorial or example about using PMF method in gromacs to obtain free binding energy? If so, please address me. Best regards -- gmx-users mailing listgmx-users@

[gmx-users] how to obtain binding energy?

Dear Justin thanks for your attention *Do you mean binding constants? * yes, I mean Ka or Kd. what about protein-dna complex? can I use PMF or TI for that to obtain binding free energy? best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] how to obtain binding energy?

Dear mohsen thanks for your reply. I forgot to say there are water and ion in my system. with new conditions, can I use PMF or TI? I have another question: is there this possibility to obtain affinity between protein and ligand by gromacs? please guide me about that. best regards -- gmx-user

[gmx-users] how to obtain binding energy

Dear gromacs users my simulation system is protein-ligand. I did 3 simulations. protein only, ligand only and protein-ligand complex. I want to know how to obtain binding energy between protein and ligand by MD simulation using gromacs. any help will highly appreciated. -- gmx-users mailing

[gmx-users] g_hbond -ac -life

Dear Erik thanks. thus -ac is only for determine the rate for hb breaking. is it true? or there is other usable case for -ac option? -- 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

[gmx-users] g_hbond -ac -life

Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB li

[gmx-users] g_hbond -ac -life

Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB life

[gmx-users] hblife.xvg and hbac.xvg files

Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] hblife.xvg and hbac.xvg files

Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] difference between p(t) and c(t)

Dear all I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB lifetime? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs

[gmx-users] g_hbond / hbmap.xpm file

Dear Justin Thus, if there are 40 hydrogen bond. Numerical indice 5 on the y-axis of .eps file is same to indice 35 in .ndx file. Is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] g_hbond / hbmap.xpm file

Dear Erik and Justin Thanks for your time and attention. My xpm file is following state: /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: "Hydrogen Bond Existence Map" */ /* legend: "Hydrogen Bonds" */ /* x-label: "Time (

[gmx-users] g_hbond / hbmap.xpm file

Dear gromacs users I used g_hbond -f *.xtc -s *.tpr -n *.ndx -hbm hbmap.xpm for hydrogen bond analysis. then I used xpm2ps -f hbmap.xpm -o hbmap.eps.the ps file is hydrogen bond index vs time. I don't understand numbers in vertical axis. do these numbers in vertical axis relate to hbond.ndx fil

[gmx-users] g_hbond / hbmap.xpm file

Dear Erik Thanks for your attention. What is your mean of [but keep in mind that the matrix is displayed with the first row at the bottom]. Please clarify that more. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arch

[gmx-users] g_hbond / lifetime

Dear Dallas Warren Thanks for your attention. Thus, if I select a certain hydrogen bond from *.ndx file, g_hbond give me HB lifetime only for that certain hydrogen bond. Is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please se

[gmx-users] g_hbond / lifetime

Dear all I used g_hbond for analysis of hydrogen bonds between protein-ligand complex. g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm -don -dan -life -nhbdist after using g_hbond, gromacs gives me: HB lifetime = 16.82 ps this lifetime is related with what hydrogen bon

[gmx-users] trjconv -pbc/box /solvent

Dear Justin in my case only -pbc nojump fix problem. my purpose is not visualization. do this xtc file ,in which protein diffuse out from box, cause any problem in analysis? if yes, how can I fix it? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] trjconv -pbc/box /solvent

Dear Justin thanks for your attentions In my case, after md simulation my protein diffuse out from one side of box. for solution I used trjconv -pbc nojump. then problem fixed but box disappears and water molecules recedes from protein. -- gmx-users mailing listgmx-users@gromacs.org http://l

[gmx-users] trjconv -pbc/ box/ solvent

Hi gromacs users I want to know after using trjconv -pbc, box disappears and solvent molecule recedes from solute. is it true? -- 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/Mailin

[gmx-users] yes/no

Dear Justin thanks thus, if I want to set 800 ps for -dump, -dump 796 is true (every frame is 4 ps). ok? -- 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 befor

[gmx-users] yes/no

Dear Justin I understood. for instance, in trjconv -dump (-1), What does it mean? -- 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 p

[gmx-users] yes/no

Hi Justin thanks for your attention. in editconf instance, if I don't use -c, this is same mean with -noc? In third column of Other opthions, somewhen, 1 and -1 is seen. What does 1 mean? What does -1 mean? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

[gmx-users] yes/no

Hi gromacs users In gromacs manual, in appendix section, for every tool, in Files section, there are input and output files needed for analysis. but in Other options section, there are some things that I don't understand. Is third column of Other opthions default values? In third column of Other

[gmx-users] -pbc nojump

Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search th

[gmx-users] Gibbs free energy of binding

Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? -- 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

[gmx-users] -tu flag in g_hbond

Dear Justin *excuseme this email is true.* I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: "Hydrogen Bond Existence Map" */ /* legend: "Hydrogen Bonds

[gmx-users] -tu flag in g_hbond

Dear Justin I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: "Hydrogen Bond Existence Map" */ /* legend: "Hydrogen Bonds" */ /* x-label: "Time (ns)" */

[gmx-users] -tu flag in g_hbond

Dear Justin thanks for your attention. this file that I want to be as ns is hbmap.xpm I did following steps to obtain pdf file : 1) xpm2ps 2) ps2pdf can I open xpm file by xmgrace? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

[gmx-users] -tu flag in g_hbond

Hi gromacs users in g_hbond command there is not -tu flag and I want to have time unit as ns no default form (ps). What is the best way to do this? Please suggest. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] g_rama / mult

Dear Tsjerk Wassenaar thanks for your attentions. ok. [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] is my actual command line. I get tpr file by command : grompp -f *.mdp -c *.gro -p *.top -n *.ndx -o *.tpr where I should put multiplicity of 3 (what file) ? -- shahab -- gmx-users mai

[gmx-users] g_rama / mult

Hi all I used [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of protein. gromacs give me rama.xvg as output but during calculation : Found 68 phi-psi combinations Dihedral around 9,11 not found in topology. Using mult=3 Dihedral around 11,18 not found in topology. Using mult=3 Dih

[gmx-users] B-factor

Dear Erik Marklund thanks for your attention I saw www.pdb.org. there is b-factor in pdb files being in this website but pdb file obtained form g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq command, has not B-factor. my bfac.pdb file is as follows : TITLE Protein in water REMARK THIS IS A SIMU

[gmx-users] B-factor

Dear *Erik Marklund* what do you meant from See the reference for the pdb file format? is b-factor a file? please guide me more. I am beginner in gromacs. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://w

[gmx-users] B-factor

Hi all I want to calculate B-factor using g_rmsf command as follows g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Pl

[gmx-users] B-factor

Hi all excuse me for my past incomplete email. I want to calculate B-factor using g_rmsf command as follows: g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq this command give me a pdb file whereas I want to obtain text file (numeral value of B-factor ). how to obtain B-factor value from this p

[gmx-users] selection of group in do_dssp

Dear gromacs users When I used do_dssp for my protein analysis, gromacs asked me [select a group]. what is the best group for this command? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the a

[gmx-users] helical parameters for DNA

Hi gromacs users I want to simulate pr-dna by gromacs.I read a article (Biophysical Journal 87(6) 3799–3813) inwhich helical parameters for DNA (rise, slide, twist, roll, tilt, shift) calculated by md simulation, but I did not understand two things: How and what command these parameters were cal

[gmx-users] PBC

used the following command: trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol but it is not working. Is there any other method or command which I could implement pbc in trajectory. Thanks in advance Morteza Shahab Shariati wrote: You can use other flags of trjconv

[gmx-users] separation of two strands of DNA during of simulation

Dear Justin thanks for your attention. You said that separation of two strands of DNA during of simulation is a normal consequence of periodic boundary conditions. I had used periodic boundary condition in mdp file as following: Periodic boundary conditions: pbc = xyz Should I dele

[gmx-users] separation of two strands of DNA during of simulation

Hi gromacs users I runing md simulation of DNA for 20 ns (5000 frame). I see trajectory during simulation. I see in some times, two strands of DNA are seprated. simulation now is in frame of 4600. is this state true and rational? any help will highly appreciated! -- gmx-users mailing listgmx

[gmx-users] simulated annealing (SA)

Hi gromacs users 1) after doing simulated annealing simulation, who can I understand that obtained structure is in global minimum and not in local minimum? 2) who can I understand that parameters used in mdp file (annealing_npoints, annealing_time, annealing_temp) are true? Any help will highly

[gmx-users] gen_vel

Hi gromacs users I want to simulation of pr-dna as follows: 1) energy minimization 2) equilibration 3) full md. Should I use gen_vel=yes in mdp files for both (2) and (3) steps? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

[gmx-users] mdp file

Hi gromacs users I want compare simulation of protein with simulation of protein-dna. should conditions (mdp file[T, P, dt, steps, ..] and box size) be same in two simulations? thanks alot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] NMR and X-ray structures

Hi gromacs users I want to simulate protein-dna interaction. but pdb file of my protein has 20 models. why pdb structures determined by NMR method consist of several models whereas pdb structures determined by X-RAY diffraction method consist of one model? Any help will highly appreciated! -- g

[gmx-users] rigid or flexible water models

Dear Justin application of SETTLE algorithm is equal to rigidity. is it true? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe r

[gmx-users] rigidn or flexible water models

Hi gromacs users Is TIP3P water model rigid? rigidity means deletion of bonded interactions. is it true? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/sear

[gmx-users] Force constant for position restraints

Hi gromacs users there is a option in pdb2gmx command : -posrefc (Force constant for position restraints). and also there is following lines in top file: #ifdef POSRES #include "posre.itp" #endif which of them is better way for position restraint simulation and determining of force constant? Any

[gmx-users] amber 03 forcefield

Hi gromacs users I will use amber 03 forcefield for simulation of protein-dna interaction. but why ffamber03.atp is as follow : amber99_0 1.00800 ; H0 H aliph. bond. to C with 1 electrwd. group (03GLY) amber99_1 79.9 ; BR bromine amber99_2 12.01000 ; C sp2 C carbo

[gmx-users] simulated annealing (SA)

Hi gromacs users about SA simulation, I saw in some papers that annealing _time is very short. fpr example [The temperature was increased from 0 to 600 K over the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps in simulation of protein-dna]. Is there limitation in ele

[gmx-users] simulated annealing (SA)

Hi all Simulated annealing consists of heating and gradually cooling steps. What is maximum temperature that we can use for heating in SA simulation of protein. Any help will highly appreciate. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gm

[gmx-users] simulated annealing (SA)

Dear Justin thanks for your attention In mdp file, if annealing_temp and annealing_time values are as follow: annealing_temp = 200 700 600 500 400 300 annealing_time =03040 506070 so, dt and nsteps have to determine such that time of SA simulation be 70. is it true? -

[gmx-users] simulated annealing (SA)

Hi all For simulated annealing simulation, except things mentioned as follow,what things should be in mdp file? integrator dt nsteps annealing annealing npoints annealing time annealing temp tcoupl tc_ grps tau_t ref_ t Any help will highly appreciated! -- gmx-users mailing listgm

[gmx-users] simulated annealing (SA)

Hi all I have some questions about simulated annealing (SA): 1) Is SA a optimization method? or a minimization method? 2) Steps in md simulation are as follow: (a) minimization (b) equilibration (c) production run (d) analysis so, where do SA lie in previous line? (before or after minimizatio

[gmx-users] cross-correlations as a function of interatomic distance

Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pleas

[gmx-users] cross-correlations as a function of interatomic distance

Hi gromacs users After using g_covar for obtaining dynamic cross correlation map, how is obtained cross-correlations as a function of interatomic distance? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pleas

[gmx-users] g_hbond

I used g_hbond for analysis of hydrogen bonds. g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm -don -dan -life -nhbdist -a 30 -r 0.35 Following text was turned up: ACF 288/288 Normalization for c(t) = 0.0204067 for gh(t) = 8.10294e-06 WARNING: Correlation fu

[gmx-users] energy minimization

Hi gromacs users I want to study interaction of protein-dna by gromacs. For energy minimization, is using of only 1 algorithm, for example steepest descent or conjugate gradient, enough? How many steps is necessary for EM? Any help will highly appreciated! -- gmx-users mailing listgmx-user

[gmx-users] temperature

Hi gromacs users I want to run simulation of protein-dna interaction. what is best for temperature in mdp file: 1) 300K (default) 2) 310k (physiologic temperature) Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] best interval for saving configurations ?

Hi all What is the best interval for saving configurations in full md step? (every what ps?) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)s

[gmx-users] SPC model for water, is suitable for amber03 force field?

Dear Justin thanks for your attention therefore, should I use tip3p.itp file from http://chemistry.csulb.edu/ffamber/ and spc216.gro from top in gromacs program? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] SPC model for water, is suitable for amber03 force field?

Hi all How I can obtain tip3p.itp and tip3p.gro files for amber force field to use them in gromacs program for simulation? there are tip3p.itp and tip3p.gro files in top folder of gromacs which are suitable for gromacs force fields no amber force fields. -- gmx-users mailing listgmx-users@gr

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