[gmx-users] g_dist without output file
Dear all When I use g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5, program was done without error, but it don't create output file (dist.xvg) in the directory in which g_dist tool was run. What is reason of this case? 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_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_spatial (gromacs 4.5 manual)
Dear gromacs users I read g_spatial tool of gromacs 4.5 manual. I have many questions. There are in the manual: USAGE: 1. Use make ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans 4. run g spatial on the xtc output of step #3. 5. Load grid.cube into VMD and view as an isosurface. In the step 2, [-center tric -ur compact -pbc none] is true or [-center -ur compact -pbc none]? In determination of SDF, there are 2 groups: for example; SDF of the first (1) group around second (2) group. In the step 2 of above usage, we should select two groups of the index file, for centering and for output. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case (all of the system). In the step 3 of above usage, we should select two groups of the index file, for least squares fit and for output. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case (all of the system). In the step 4 of above usage, we should select two groups of the index file, to generate SDF and to output cords. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case. Please answer my question exactly with determining group numbers in the each step. Any help will highly appreciated. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dist without output file
Dear Lina Thanks for your reply. Without the -dist 0.5, I get the -o dist.xvg output, but I need list of the all atoms in group 2 closer than dist to the center of mass of group 1. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dist without output file
Dear Lina There is not any things related to list of atoms on the terminal. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dist without output file
Dear Lina Very thanks for your time and attention. Initial command was : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5 After running following command the problem was solved : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 5 t: 17008 6773 NA 21881 NA 3.05534 (nm) t: 17008 6774 NA 21882 NA 3.27381 (nm) t: 17008 6775 NA 21883 NA 2.44312 (nm) t: 17008 6776 NA 21884 NA 2.0746 (nm) Last frame 2 time 17008.000 Now, I have a general question. In some of gromacs tools, there is distance parameter. I want to know what is dimension of the distance in gromacs? nm or A? Best regards -- 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] RMS fluctuations and error estimate from block averaging
Dear all I have a question about g_analysis with option -ee. What is difference between RMS fluctuations and error estimate obtained from block averaging? Best regards -- 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] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and [CGLN] in rtp file of amber03 force field. Should this single residue be as both of [NGLN] and [CGLN]? How to fix this error? 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_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] distance and angle cutoff for hydrogen bond
Dear gromacs users in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor - Donor - Hydrogen) -r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)] I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A. and angle of 30 = acceptor-donor–hydrogen angle. is my think true? if I want following criterion for hydrogen bond analysis, is [ -r 3.5 and -a 135 ] true? donor-acceptor distance (dDA) ≤ 3.5 Å and the donor–hydrogen-acceptor angle (αDHA) ≥ 135°. 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_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] position restrained minimization on the one part of a system
Dear all my system contains protein + ligand+ water molecules. protein + ligand = solute water molecules = solvent I want to do minimization energy in 3 steps : step 1) on protein only step 2) on all solute (protein + ligand) step 3) on all system should I use position restrained minimization energy and use define = -DPOSRES in mdp file? if so, what is my mdp file for each of 3 steps? # step 1: ??? please complete this section. # step 2: define = -DPOSRES_WATER # step 3: I don't use -DPOSRES. In posre.itp file, what is suitable value for force constant? best regards -- 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] position restrained minimization on the one part of a system
Dear Mark thanks for your reply you said "if pdb2gmx is able to treat the whole system in one pass, then it will write such position restraint files automatically" in my system, what pdb2gmx includes are in below: ; Include forcefield parameters #include "amber03.ff/forcefield.itp" ; Include chain topologies #include "complex_Protein_chain_A.itp" #include "complex_DNA_chain_B.itp" ; Include Position restraint file #ifdef POSRES #include "posre_Protein_chain_A.itp" ; Include Position restraint file #ifdef POSRES #include "posre_Protein_chain_B.itp" ; Include water topology #include "amber03.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber03.ff/ions.itp" [ system ] ; Name complex [ molecules ] ; Compound#mols Protein_chain_A 1 DNA_chain_B 1 SOL3500 unfortunately, I don't know about step 1. please guide me about that. -- 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] position restrained minimization on the one part of a system
I want to use define = -DPOSRES_Protein_chain_A for step 1. 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/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] position restrained minimization on the one part of a system
Dear Justin thanks for your attention I deleted posre.itp file which pdb2gmx was created (containing all solute).I made a posre.itp (containing only protein) by genrestr. now if I use define = -DPOSRES, gromacs use from my posre.itp. 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/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] trjconv to remove periodicity (KALP15 in DPPC tutorial)
Dear Justin I do your tutorial entitled " KALP15 in DPPC ". In Step Three: Defining the Unit Cell & Adding Solvent, You said "Use trjconv to remove periodicity ". When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact, gromacs tell me: Select group for output. Which group I should select? system or dppc? Best wishes -- 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] trjconv to remove periodicity (KALP15 in DPPC tutorial)
Dear Justin Thanks for your quick reply. I want to study a system containing DOPC and cholesterol and drug. I correctly prepared gro files and topology parameters for this system. I did previous step (Step Two: Modify the Topology) without problem. I have 2 problems. 1) After I use trjconv -s em.tpr -f dopc_chol.gro -o dppc_chol_whole.gro -pbc mol -ur compact, When I see dppc_chol_whole.gro using vmd, almost 5 DOPC emerg lipid structure. 2) In your tutorial, system contains DPPC and KALP and you used: perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat But in my case, system contains DOPC and cholesterol and drug. How to do these steps (Scale and shrink the lipid positions)? Best wishes -- 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] trjconv to remove periodicity (KALP15 in DPPC tutorial)
Dear Baptiste Very thanks for your reply. Unfortunately, I have not access to InflateGro2. I encountered with error. If there are a script for InflateGro2 like InflateGro. please sent me perl script related to InflateGro2. Best wishes. -- 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] LAMBADA and InflateGRO2
Dear gromacs users I want to use LAMBADA and InflateGRO2 to create a system containing dopc lipid + cholesterol + drug. When I use ~/lib/lambada/lambada_rc1/lambada -f1 drug.gro -f2 lipid_chol.gro I encountered with Illegal division by zero at /home/karami/lib/lambada/ lambada_rc1/lambada line 677. How to resolve this issue? Please help me to do this step. Best wishes -- 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] fftw
Dear gromacs users Why should I install fftw before gromacs installation? I want to know exact role of fftw in gromacs calculations. Please guide me about that. Best wishes -- 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] emstep unit
Dear gromacs users What is the reason of this point that unit of the emstep (step size)is nm? I think ps (unit of time) is more resonable. If I am wrong, please give me explanation about this point. -- 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] emstep unit
Dear Justin Thanks for your reply. Ok. You are right. There is no "time" during EM. For example, if I use nstep = 10,000 and emstep = 0.01, what means of Step size in this case, exactly? Please give me more explanation. 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.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] time evaluation of dimensions of the simulation cell
Dear gromacs usres I am doing simulation of lipid bilayer. I did 2 steps: 1) energy minimization, 2) equilibration. Before production run, I want to monitor dimensions of the simulation cell to test the stability of the simulation. On the other hands, I want to plot dimensions of the simulation cell as a function of time. What tool of gromacs is appropriate for obtaining time evaluation of dimensions of the simulation cell? How to do this? Any help will highly appreciated. Best wishes. -- 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] Invalid order for directive defaults
Dear all My system contains protein + cnt + water molecules. I have summarized what I did below: --- 1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then I converted it into pr.itp by deleting ; Include forcefield parameters #include "charmm27.ff/forcefield.itp" from begining of file and by deleting ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 from ending of file. 2) I used bonded and nonbonded parameters for cnt from paper: J. Phys. Chem. B 2001, 105, 9980-9987 (Carbon Nanotubes in Water: Structural Characteristics and Energetics). I created cnt.ff folder containing following files: ffcnt.atp / ffcnt.n2t / ffcnt.rtp / ffcntbon.itp / ffcntnonbon.itp / forcefield.itp Then, I put cnt.ff folder in GMXLIB directory. 3) By g_x2top and cnt.ff created in previous step, I obtained cnt.top for cnt then I converted it into cnt.itp by deleting ; Include forcefield parameters #include "cnt.ff/forcefield.itp" from begining of file and by deleting [ system ] ; Name CNT [ molecules ] ; Compound#mols CNT 1 from ending of file. 4) I combined cnt and protein to create one coordination file (system.gro). Order of molecules are as follows: 1) cnt 2) protein 3) water. 5) I wrote a topol.top file given below, ; Include forcefield parameters #include "cnt.ff/forcefield.itp" #include "cnt.itp" #include "charmm27.ff/forcefield.itp" #include "pr.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name CNT/Protein/SOL [ molecules ] ; Compound#mols CNT 1 Protein 1 SOL 1359 When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with following error: Fatal error: Syntax error - File forcefield.itp, line 11 Last line read: '[ defaults ]' Invalid order for directive defaults Content of forcefield.itp in cnt.ff directory is as follows: *** *CHARMM port writted by * *Par Bjelkmar, Per Larsson, Michel Cuendet, * *Berk Hess and Erik Lindahl. * * Correspondance: * *bjelk...@cbr.su.se or lind...@cbr.su.se * *** #define _FF_CNT [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #include "ffcntnonbon.itp" #include "ffcntbon.itp" and Content of forcefield.itp in Charmm27.ff directory is as follows: *** *CHARMM port writted by * *Par Bjelkmar, Per Larsson, Michel Cuendet, * *Berk Hess and Erik Lindahl. * * Correspondance: * *bjelk...@cbr.su.se or lind...@cbr.su.se * *** #define _FF_CHARMM [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #include "ffnonbonded.itp" #include "ffbonded.itp" #include "gb.itp" #include "cmap.itp" ; Nucleic acids nonbonded and bonded parameters" #include "ffnanonbonded.itp" #include "ffnabonded.itp" In both of forcefield.itp files, line 11 is [ defaults ]. I changed name of forcefield.itp file in cnt.ff directory to cntff.itp, but there is same error, again. That is all what I exactly did. Is anything wrong or missing? How to solve this error?
[gmx-users] Invalid order for directive defaults
Dear Justin Very thanks for your reply. I created a new topol.top file as below: 1) I used once default directive. 2) I put cnt.itp file in working directory. 3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp" in the end of topol.top file. I modified [ molecules ] directive. -- begining of topol.top file is as follows: ; Include forcefield parameters #include "charmm27.ff/forcefield.itp" [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] . . . . end of com.top file is as follows: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif #include "cnt.itp" ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 CNT 1 SOL 1388 --- Previous error (Invalid order for directive defaults) was solved, but When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with this error: ERROR1 [file cnt.itp, line 2861]: No default Angle types . . . . . . ERROR 1218 [file cnt.itp, line 4078]: No default Angle types Fatal error: There were 1218 errors in input file(s). Lines 2861-4078 are related to [ angles ] directive in cnt.itp file. How to solve this issue? 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_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] Invalid order for directive defaults
Dear Justin My cnt is infinite. I obtained cnt.top by g_x2top and then modified cnt.top to cnt.itp. For obtaining cnt.top, I used following files: --- ffcnt.atp: CA 12.01100 ; aromatic C --- ffcnt.n2t: CCA0.0012.011 3C 0.141 C 0.141 C 0.141 CCA0.0012.011 2C 0.141 C 0.141 --- ffcntbon.itp: [ bondtypes ] ; i j funcb0 kb CA CA 3 0.1418 47890.0 21.867 [ angletypes ] ; i j k functh0 cth ub0 cub CA CA CA 2 120.00 562.20 [ dihedraltypes ] ; i j k l funcphi0cp mult CA CA CA CA 5 0.00 25.12 0.00 0.00 --- ffcntnonbon.itp: [ atomtypes ] ;name at.num masscharge ptype sigma epsi CA 6 12.011000.00A 0.385 0.4396 --- In cnt.itp file, angle section of file is as follows: [ angles ] ; aiajak functc0c1c2c3 2 1 8 1 2 1 287 1 8 1 287 1 1 2 3 1 1 210 1 3 210 1 2 3 289 1 2 3 406 1 289 3 406 1 5 417 1 5 4 320 1 17 4 320 1 4 5 6 1 . . . . . . I saw system.gro file by VMD, there are all angles defined above in [angle] directive. -- 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] Invalid order for directive defaults
Dear Justin Thanks for your reply. > In your previous setup, you were effectively trying to use CHARMM27 + some > other > force field related to the CNT. You can't do that. Thus, Gromacs is not appropriate for systems containing cnt. Is my deduction true? In my case, peptid + cnt + water molecules, what is your suggestion? Please guide me and explain more. How to do MD simulation of my system by gromacs? 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_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] Invalid order for directive defaults
Dear Justin Thanks for your quick reply. I was confused. If I add #include "ffcntbon.itp" after #include "cnt.itp" in .top file, my problem was solved and error was solved? -- 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] residence time of water molecule and life time of hydrogen
Hi gromacs users I am beginner in gromacs. I did md simulation of a protein by gromacs and now I want to obtain residence time of water molecule and life time of hydrogen bonds. Can I obtain both of them using gromacs? please guide me by detail. -- 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] residence time of water molecule and life time of hydrogen
*Dear Justin* ** *I read manual and specially g_hbond. but manual doesn't gime me information about * residence time of water molecule and life time of hydrogen. -- 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] trjconv -pbc
Hi gmx users Perhaps, this question be repetitive. I want to know using trjconv -pbc is only a solution for visualization problem? Is there feasibility to use old trajectory file (with out trjconv -pbc) for any kind of analysis without any problem? -- Atila Petrosian Ph.D. student of BioPhysical Chemistry University of Oulu,Finland -- 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] -b -e
Dear gromacs users my simulation time is 10 ns (1 ps), but, I want to use last 4ns for analysis. for example, if I use g_rms -b 6000 -e 1 -o rmsd.xvg, in xvg output file, rmsd plotted versus time (from 6000 to 1 ps in horizontal axis). while I want horizontal axis be from 0 to 4000 ps. how to do it? -- 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] -don (g-hbond)
Dear Justin Header of file is as follow: @title "Donor properties" @xaxis label "Time (ps)" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Nbound" @ s1 legend "Nfree" 1.950e+04 18 185 1.950e+04 17 186 1.951e+04 19 184 1.951e+04 16 187 1.952e+04 18 185 1.952e+04 17 186 1.952e+04 16 187 1.953e+04 18 185 1.953e+04 18 185 What do Nbound and Nfree denote exactly? summation of Nbound and Nfree is constant. what is that (summation)? -- 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] -don (g-hbond)
Hi all I want to know regarding 2nd and 3rd column of donor.xvg output about g_hbond -don. -- 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] -don (g-hbond)
Dear Justin I confused. number of donors in donor.xvg file is 203. while, when use g_hbond: found 143 donors. Select a group: 2 Selected 2: 'Protein_A' Select a group: 3 Selected 3: 'Protein_B' Checking for overlap in atoms between Protein_A and Protein_B Calculating hydrogen bonds between Protein_A (1042 atoms) and Protein_B (825 atoms) Found 143 donors and 439 acceptors Making hbmap structure...done. Reading frame 0 time 19500.000 Will do grid-seach on 14x14x14 grid, rcut=0.35 Reading frame 120 time 19980.000 Found 40 different hydrogen bonds in trajectory Found 69 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 143/143 - Reduced number of hbonds from 40 to 40 - Reduced number of distances from 69 to 69 Average number of hbonds per timeframe 19.310 out of 31388.5 possible -- 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] y-axis label in hbang and hbdist.xvg file
Dear Justin very thanks for your attention. I have another question about g_hbond. in manual, -dist and -ang are distance and angle distribution of all hydrogen bonds respectively. I want to know in hbang and hbdist.xvg file, what is y-axis label? -- 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] y-axis label in hbang and hbdist.xvg file
Dear Justin count = count of hydrogen bonds being in a certain distance (between 0-0.35) and angle (between 0-30)? -- 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] water molecules (interfacial)
Dear all my system includes protein, ligand and water. I want to obtain number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand. -- 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] water molecules (interfacial)
Dear Mark and gromacs users thanks for your time and attention. how to make selection.dat file? what should be in that? please clarify this new tool more. how can I obtain what I need (number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand)? -- 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] water molecules (interfacial)
Dear Justin are you sure g_dist -dist give me what I need. if so, how? since, dist.xvg gives distance vs time and lifetime.xvg gives number of contact vs time. while, I want number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand. -- 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] water molecules (interfacial)
Dear Justin I used g_dist -f .xtc -s .tpr -n .ndx -o -lt -dist 1 but program give me only lifetime.xvg. there are no dist.xvg file. why? -- 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] .psf and .dcd files
Dear gromacs users I did simulation of protein-ligand by gromacs 4.0.7 with amber 03 forcefield. I need to .psf and .dcd files. can I convert/obtain them? 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_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] .psf and .dcd files
Dear Ran thanks for your reply. Is psfgen a separately program? -- 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] residence time of water molecule
Hi how to obtain residence time of water molecule using md simulation and gromacs? What is the best way to do this? Please suggest. -- atila -- 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 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/mailing_lists/users.php
[gmx-users] contact map
Hi gromacs users after simulation of protein-ligand, in analysis section, how to obtain contact map for protein-ligand? thanks in advance. -- atila -- 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 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/mailing_lists/users.php
