[gmx-users] residue index

hi all, I want to calculate the contact in a index group by g_mdmat. However, the residue index is not continuous in it because this index group is a combination of two subunits(subunit1: residue 1-470, subunit2: residue 2000-2470). When I use g_mdmat, a very huge matrix is produced and a lot

Re: [gmx-users] g_covar

Mark Abraham wrote: tangxuan wrote: Mark Abraham wrote: tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in w

Re: [gmx-users] g_covar

Mark Abraham wrote: tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in what for

Re: [gmx-users] g_covar

Berk Hess wrote: This is an incorrect warning, which has been introduced in version 3.3.2. I have corrected the warning for 3.3.3. Berk. Date: Wed, 9 Jan 2008 14:51:52 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] g_covar Dear all, When I am using g_covar to

[gmx-users] g_covar

Dear all, When I am using g_covar to calculate the covariance matrix for alpha carbons in one subunit of my protein, I get a warning" WARNING number of atoms in tpx (929) and trajectory (293401) do not match". 929 is the alpha carbon number and 293401 is whole system atom number. In the comma

Re: [gmx-users] g_rmsf fitting

Thanks for your detailed explanation. Sorry for my words and I wrote them in a hurry without careful check. In fact, I can not see a whole protein in ref1.tpr and part of subunits are out of box. I do not know if this can be called jump. Tang Tsjerk Wassenaar wrote: Hi Tang, The subuni

Re: [gmx-users] g_rmsf fitting

between the two reference structures? Cheers, Tsjerk On Jan 3, 2008 3:37 PM, tangxuan <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: Hi, Does anyone know how fitting step works in detail when running g_rmsf? When I used two different tpr files with same prot

[gmx-users] g_rmsf fitting

Hi, Does anyone know how fitting step works in detail when running g_rmsf? When I used two different tpr files with same protein structure but different atoms position, the result is very different. Can you explain this ? many thanks! Tang ___ gmx-

Re: [gmx-users] pbc and tpr file

then have a look. > Actually, you should've done this prior to removing jumps from the > trajectory, since you must be sure to remove the jumps in the right > way (check the archives for more discussion on these issues). > > Cheers, > > Tsjerk > > On Dec 12, 2007 1:42 AM,

[gmx-users] pbc and tpr file

hi all, I want to calculate the rmsd of my protein. If I remove the jump in the xtc file or trr file, what should I do with tpr file? Thanks. Tang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] pbc problem

hi, all My protein has 16 subunits. After I use trjconv '-pbc nojump' to remove the jump in the whole protein, there are no jump to each subunits. However, when i check pdb file of the first frame, it is shown that the subunits are not in right position. The area of interface between some subunits

[gmx-users] G_sas reside area

Hi,all Is there a fast way to compute the resides area at each time in the simulation process? I can get the resides area at some specific time, a slow way.For exmple, when I get the average reside area between 0 ps and 100ps and average reside area between 0 ps and 101 ps, i can get the reside a

Re: [gmx-users] g_sas problem

many resides between three ps. Maybe the big changes of total SAS in interaction region at 15938 ps is because of big size of two subunits(each has 471 resides). What is your idea? Thanks, Tang jiaowei On Wed, 2007-10-31 at 01:59 +1100, Mark Abraham wrote: > tangxuan wrote: > > Yes, th

Re: [gmx-users] g_sas problem

22 15966 1.262 15967 1.235001 15968 1.32900 Thanks for your help. Tang jiaowei On Tue, 2007-10-30 at 14:57 +0100, David van der Spoel wrote: > tangxuan wrote: > > Dear,all > > When I calculate the accessible surface area(ASA) of interaction region > &g

[gmx-users] g_sas problem

Dear,all When I calculate the accessible surface area(ASA) of interaction region between two subunits A and B in my protein. First I calculated the ASA of A and B by "g_sas -f .xtc -s .tpr -n index.ndx -o .xvg -n index.ndx" respectively. After that, I combined A and B as the one group, then I compu

Re: [gmx-users] g_rmsf and pbc

this simulation,the subunits are separate in the first frame. Do you have any other methods to solve this problem? On Tue, 2007-10-23 at 17:18 +0200, David van der Spoel wrote: > tangxuan wrote: > > Mark,thanks for your reply. I am not sure what happened and I can show > > you

Re: [gmx-users] g_rmsf and pbc

Tang jiaowei On Wed, 2007-10-24 at 00:43 +1000, Mark Abraham wrote: > tangxuan wrote: > > Dear all, > >The protein I am working on is rubisco, consisting of 8 identical > > large subunits and 8 identical small subunits. I try to calculate RMSF > > for each large subunits

[gmx-users] g_rmsf and pbc

Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I fo

[gmx-users] b-factor

Dear all, I have got a pdb file by command g_rmsf and option -oq, and the content of the file is like this: TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 148.918 148.918 148.428 59.89 59.89 90.00 P 1 1 MODEL1 ATOM 47354 CA ALA I9967 60.915 88

[gmx-users] pbc problem

Dear all, If pbc is full or xyz in mdp file, do i need to use the "trjconv -pbc nojump" to remove the jump when the protein is separate in the box after simulation and I want to calculate the rmsd of the protein? What is difference of use of pbc in mdp file and in "trjconv -pbc nojump"? Thank

Re: [gmx-users] remove periodic boundary in tpr file

> after running pdb2gmx)? > By the way, if you removed the jumps over the boundary (you don't > really want to remove periodicity :p) you must already have a proper > structure. Or you can then extract the first frame from the trajectory > and use that as the starting point. >

[gmx-users] remove periodic boundary in tpr file

Dear all, I am try to use g_rms to a protein, but its start structure in the simulation is not in one box. I removed the periodicity for the xtc file by trjconv, but do not know how to remove the periodicity in the tpr file. Could you give me some suggestions? Thank you. Jiaowei Tang ___

[gmx-users] G_hbond and periodicity

Hi all, Does periodic boundary affect the calculation of hydrogen bond if my protein is not in one box? What about other calculations? Thank you, Tang jiaowei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/list