[gmx-users] MD Simulations

Dear friends, Please read nice article on MD Simulations http://www.springerlink.com/content/6jt0843463226321/ -- Pawan -- 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_Li

[gmx-users] Please rectify free energy problem

g_lie calculates the deltaG= alpha(p - w) + beta(p - w) equation. But when calculating DGbind from g_lie it will ask for only one term at a time i.e. -Elj for either p or w and -Eqq for either p or w. My question is when using only p for -Elj and Vl-s el>p for -Eqq, how the LJ and EL terms calcul

[gmx-users] g_lie

g_lie calculates the deltaG= alpha(p - w) + beta(p - w) equation. But when calculating DGbind from g_lie it will ask for only one term at a time i.e. -Elj for either p or w and -Cqq for either p or w. My question is when using only p for -Elj and Vl-s el>p for -Cqq, how the LJ and EL terms calcul

[gmx-users] Free energy

g_lie calculates the deltaG= alpha(p - w) + beta(p - w) equation. But when calculating DGbind from g_lie it will ask for only one term at a time i.e. -Elj for either p or w and -Cqq for either p or w. My question is when using only p for -Elj and Vl-s el>p for -Cqq, how the LJ and EL terms calcul

[gmx-users] Installation error

I have already posted this error report on 6 Dec 2010 but still have not getting any solution. So I am thankful if any one can rectify the solution of installation problem i.e. While installing gromacs-4.5.3 I got an error on executing make command. I am installing this gromacs version on cygwin. T

[gmx-users] Extreme

Dear tsjerk, I am very sorry to say that your suggestions does not help but increase confusions only. I am highly obliged if you give me clear statements about the scores to understand this concept in depth. I have searched research article about this concept but failed to find even an single arti

[gmx-users] Extreme

trajectory by using G_anaeig. Give me some clue about these minimum/maximum scores.Can i consider thhis mimimum or maximum structure as a native structure? Pawan Raghav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] g_anaeig

Dear justin, Thanks for your useful suggestions but not the right way to post these things. Anyway Dear I have already read the link mentioned by you and know very well what does -extr do actually I want to extract some minimum energy structure for docking studies from 12500 ps to 15000 ps MD traj

[gmx-users] g_anaeig

I am postin ths question second time so please solve this issue g_anaeig generated numbers of c-alpha or protein structures through -extr extreme.pdb. The bash shell show numbers of eigenvector structures starting from first to last frames are as follows eigenvector Minimum Max

[gmx-users] anaeig

g_anaeig generated numbers of c-alpha or protein structures through -extr extreme.pdb. The bash shell show numbers of eigenvector structures starting from first to last frames are as follows eigenvector Minimum Maximum value time value time

[gmx-users] gromacs-4.5.3 installation error

Dear users, While installing gromacs-4.5.3 I got an error on executing make command. I am installing this gromacs version on cygwin. The error written below, please tell me about the error where I was wrong Creating library file: .libs/libgmx.dll.a .libs/checkpoint.o:checkpoint.c:(.text+0xcd):

[gmx-users] PR

I have read that SPC/SPCE is an rigid and pre-equilibrated 3 point water model. Is it likely mean that position restrained dynamics is not required. If we are not intersted in position restrained dynamics then what are the criteria for system needed. -- Pawan -- gmx-users mailing listgmx-use

[gmx-users] PR

Thank mark for comments, but I have check the structure after energy minimization through ramachandran plot and found 82% residues were lies in core region. After performed position restrained dynamics it reduced to 52% in core region also 1 bad contact was found. I have taken SPC water model then

[gmx-users] Position restrained..

Dear All, Hope this mail will find you in good health. I am facing a problem regarding Position restrained dynamics (PR). I have done Molecular dynamic simulation (for cytosolic protein) but has not performed PR. So i m little confused if this effects the results and if yes to what extent it effe

[gmx-users] Area per atom

Dear All Using g_sas on trajectory file with command g_sas -f .xtc -s .tpr -oa atomarea.xvg gives following output @title "Area per atom" @xaxis label "Atom #" @yaxis label "Area (nm\S2\N)" @TYPE xy 1 0.139885 0.0351154 2 0.0510893 0.0236223 3 0.0510077 0.0234374 4 0.051203

[gmx-users] contact residues

I have used g_mdmat g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg I got dm.xpm graph which shows mean of whole simulation residue contacts. How to get information about the particular residue are in contact? how to get list of contact residues? In graph file num.xvg there

[gmx-users] Please solve this

I am posting this question second time so please tell me, where I was wrong? In manual g_analyze reads an ascii file and analyzes data sets, in which input file was graph.xvg. To generate eigenvector and eigenvalue file I have used g_covar and analyzed eigenvectors by g_aneig. So according to manu

[gmx-users] g_anaeig

Thankyou so much Tsjerk Wassenaar -- Pawan -- 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 interfac

[gmx-users] minima

g_anaeig command give some minimum or maximum value are these value energy minima and maxima for extreme 2 frame structures? eigenvector Minimum Maximum value time value time 1 -9.162661 99.0 2.682097 9450.0 2

[gmx-users] g_mdmat

Dear friends, I have used g_mdmat g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg I got dm.xpm graph which shows mean of whole simulation residue contacts. How to get information about the particular residue are n contact? I mean to say, Is there any tool to give list of co

[gmx-users] g_hbond

Below is the hbond.xvg content 1 coloumn is for time second for numbers, but I am not getting for 3rd one i.e. Pairs within 0.35 nm is this shows area in cutoff range? @ title "Hydrogen Bonds" @ xaxis label "Time" @ yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ l

[gmx-users] g_analyze

In manual g_analyze reads an ascii file and analyzes data sets, in which input file was graph.xvg. To generate eigenvector and eigenvalue file I have used g_covar and analyzed eigenvectors by g_aneig. So according to manual input file should be an ascii file, is it covar.dat file generated by g_cov

[gmx-users] Essential Dynamics

Dear Tsjerk, It will be helpful to me if you would like to solve my problem I have already read your tutorial and so many papers but I am really confused and thats why mail to you. So please answer me which will help me lot to understand right concept. -- Pawan -- gmx-users mailing listgmx-

[gmx-users] essential dynamics

Hi all, I have a confusion regarding "Essential Dynamics". I have read so many papers regarding PCA and ED most of the papers among them explained eigenvectors and eigenvalues are as follows: if a protein has 207 C alpha residues then the total no of eigenvectors are 3N X 3N, where N= no. of atom

[gmx-users] PCA

I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr files. The eigenvectors were analyzed by g_anaeig program and got eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to know 1. Which file among these shows relative positional fluctuation with eigenvector in

[gmx-users] Re: PCA

On 8/14/10, pawan raghav wrote: > > I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr > files. The eigenvectors were analyzed by g_anaeig program and got > eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to > know > 1. Which file

[gmx-users] PCA

I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr files. The eigenvectors were analyzed by g_anaeig program and got eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to know 1. Which file among these shows relative positional fluctuation with eigenvector in

[gmx-users] Averege structure

I have done 15ns MD simulations at 300k temp for a protein finally obtained an average structure from g_rmsf. so please tell me is output average structure is a sampled structure? is there no need of remd or sampling further because I got plateau in RMSD calculation at last? I have strongly energy

[gmx-users] REMD

Dear Justin, I have read manual there was an equation where T1 and T2 are the two temperatrure will be assign but in my case I don't have different temperature. I have to simulate at same temperature. Is there any other alternative to perform sampling rather than REMD. I am working on one process

[gmx-users] REMD

Dear Justin, No dear I have not modelled the membrane, my protein is a simple protein which contained a loop about 59 amino acids. So I am intrested to model this loop through MD simulation. In this concerned I did 15 ns simulations, but right now don't know how to perform sampling for my protein

[gmx-users] Technical

Dear Justin, Thanks for the wonderful suggestions which is very clear and informative but I am confused about some points below 1. Actually my protein is human mitochondrial protein so I have used GROMOS 96 53a6 ff. is it correct? but you have mentioned about the condition applied, so I don't und

[gmx-users] General Question

Dear GROMACS team members, I have a general question about the GROMACS, actually I have used GROMACS for the simulation of 59 amino acids domain part of the protein containing within it. This domain lies in the position from 34-92 out of 239 residues, this loop having only 12 residues similarity w

[gmx-users] g_covar

Thanks Mark for your advice Note: The fit analysis group are identical, while the fit is mass weighted and the analysis is not making the fit non mass weighted. But, this is the the real unning out put of the command prompt Please let me know anyone what is the meaning of this note? and also tel

[gmx-users] C-alpha group

Hi friends, For ED sampling I have used mdrun command to simulate about 59 residue protein (hypothetical model) then used g_covar to get eigenvec.trr and eigenval.xvg files. But while using this command it asked to chose a group two times, so according to this I have choosed C-alpha

[gmx-users] PCA

I have a little concept problem regarding principal component analysis. So my question is about ED sampling are as follows: 1. I have read from the manual that g_covar calculates and diagonalize the (mass-weighted) covariance matrix. So what is the meaning of mass-weighted in covariance matrix? 2

[gmx-users] RMSIP

Thanks mark, but I think that g_anaeig calculates the degree of overlap then what method would you use to calculate this? -- Pawan -- 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 bef

[gmx-users] PCA

I have a little concept problem regarding principal component analysis. So my question is about ED sampling are as follows: 1. I have read from the manual that g_covar calculates and diagonalize the (mass-weighted) covariance matrix. So what is the meaning of mass-weighted in covariance matrix? 2

[gmx-users] RMSIP (Root mean square inner products)?

Please tell me how gromacs calculates degree of overlap between conformational spaces of the two proteins is it from RMSIP (Root mean square inner products)? if yes then give me the reference in gromacs tutorial 4.0 -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] pH

Dear I have defined pH = 7.0 in mdp file according to tutorial but it shows an error. what is the criteria to set the different pH in .mdp file. -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

[gmx-users] dssp problem

I have download dsspcmbi.zip and extract the dssp folder into /cygdrive/c/cygwin/usr/local/bin/ directory. Then set the environment variable export DSSP=/cygdrive/c/cygwin/usr/local/bin/dssp for bash. then I have gone to my folder by using cd where all my md files were present i.e. /cygdrive/c/grom

[gmx-users] Potein-protein complex simulations

Dear users, I am using gromacs to understand the protein-protein complex interaction stability prediction. for this I have used protein-protein docked complex as initial .pdb file to simulate. According to gromacs drug enzyme complex 3.3.1 tutorial, the .itp file needed as input f

[gmx-users] g_sas

*I executed the following command. ** **g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg *** ** *xmgrace -nxy mdrun.xvg* *I get two sets of values: one is bigger (black) than the other (red). *** *I have checked the manual and other sources, but I could not find an **answer about the black and red li

[gmx-users] GMXRC Problem

Dear Justin, I have some problem regarding GMXRC execution, I got an error while using gromacs-4.0.7 on windows vista using cygwin i.e. /usr/local/bin/GMXRC: line 35: return: can only 'return' from a function or sourced script. /usr/local/bin/GMXRC: line 44:CSH::command not found /cygdrive/c/Gro

[gmx-users] MD simulations with multiple structures

Dear Justin, I want to know about 1. How to run MD simulations with multiple structures? -- Pawan -- 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 (

[gmx-users] How to insput more than two PDB files to use for MD run

Dear, Is it possible to compare more than two pdb files MD simulations in a single run? how? -- Pawan -- 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 po

[gmx-users] GRACE

Hi, Please tell me how to install GRACE source files to execute xmgrace command to visualize 2D graph. I am unable to installed it as read from tutorial. please help me as I am in need. -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Hi

Which files should be downloaded to use GRACE and in which directory should be installed to use xmgrace command. -- Pawan -- 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 posti

[gmx-users] gmx-GRACE problem

Hi friends I want to know about which should be downloaded to use GRACE. -- Pawan Kumar Raghav -- 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] Problems

When defining the box dimention then how do I know about the distance of protein from the box wall? Which should be greater than half of the Cut-Off (1.4nm) (according to some tutorial). Then what are longest cutoff which must be shorter than half the shortest box vector to satisfy the minimum ima

[gmx-users] xmgrace

While running MD simulation I have number of queries mentioned below: 1. When executing xmgrace command it returns the bash command not found, then how to install GRACE package on windows? 2. When defining the box dimention then how do I know about the distance of protein (207 residues) from the b

[gmx-users] gromacs error

I am using Gromacs on windows hen executing pdb2gmx command, I got an error i.e. Fatal error: Atom HD1 in residue HISB 3 not found in rtp entry with 14 atoms while sorting atoms. May be different protonation state. Remove this hydrogen or choose a different protonation state. I want to know what

[gmx-users] (no subject)

I have used GROMACS 4.0.5 on windows can anyone tell me about how to get em.mdp, and pr.mdp file for my protein. -- Pawan -- 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 posti

[gmx-users] Re: gmx-users Digest, Vol 67, Issue 60

gt;> > >>> -- > >>> > >>> > >>> Justin A. Lemkul > >>> Ph.D. Candidate > >>> ICTAS Doctoral Scholar > >>> Department of Biochemistry > >>> Virginia Tech &g

[gmx-users] (no subject)

After installing gromacs4.0 on windows it created Gromacs directory containing several .exe files in bin directory. But when I used pdb2gmx command it will shows that basch command is not found. So anyone can tell me what is that. -- Pawan Kumar Raghav Bioinformatician Stem Cell and Gene Therapy

[gmx-users] gmx user

Hello Users, I am trying to install gromacs on windows and find lot of problems. First I have installed Cygwin with gcc, gdb and make packages. Then FFTW-3.2.2 and configure it but when I used make and make install commands but some directories leave as it is. When configure gromacs-4.0.5 then it

[gmx-users] gmx user

Dear all, I am a new user of GROMACS and suffering from severe problem about fftw-3.2.2 installation. Actually I have installed cygwin on windows XP with gcc, gdb, and make packages rest all are leaved default. Now when I have used configure command then it would give last line as config.status: