[gmx-users] mean square displacement

Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in :

Re: [gmx-users] regarding MSD

getting the same transition temperature but the MSD values are coming different (eg at a particular temperature if I average all the MSD values, I am getting value of 15000 while reported value is 1.5 - both values in same unit angstrom square) On Fri, Aug 22, 2014 at 7:15 PM, Nidhi Katyal

Re: [gmx-users] regarding MSD

is highly appreciated. On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve

[gmx-users] regarding g_hydorder

Hello all I would like to calculate both distance and angle water orientational order. I have made an index file containing all oxygen atoms of water and used trjorder as: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1_1 file2_1 -or file1_2 file2_2 How to interpret the results of the output

[gmx-users] regarding MSD

Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average

Re: [gmx-users] atoms are not part of any of the T-Coupling groups

in advance. Nidhi On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created

[gmx-users] atoms are not part of any of the T-Coupling groups

Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of

Re: [gmx-users] Groups in index.ndx

Use make_ndx -f *.gro -n old_index.ndx -o old_index.ndx On Fri, Jul 25, 2014 at 4:53 PM, INPE (Ingrid Viveka Pettersson) i...@novonordisk.com wrote: Dear Group, I have defined different specific groups in the index.ndx file. My problem is that if I try to add a new group, the old ones are

[gmx-users] Running job on GPUs

Hello all I am trying to run my job on 2 nodes by utilizing all available cores. On each node of the cluster, we have two GPUs and two sockets with 8 cores each. Every time I am submitting the job, we find that it is running on one node. How to make use of the other node? Till now, I have used

[gmx-users] g_hbond

Hi all, I have created hydrogen bond existence map. In the index file generated using hbn option I can see following lines at the end: 1 2 1598 1 2 1851 1 2 1852 1 2 1862 10 11 1643 10 11 1651 10 11 1658 10

[gmx-users] Hydrogen bond existence map

Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn option of g_hbond along with index file would serve the purpose. But the resulting output file is giving existence map for each atom of the residue. Instead, I

[gmx-users] binding sites with MD

Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites of ligand with protein? I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with random placement of ligand initially. In the time interval between 40 to 50ns,

Re: [gmx-users] parameters problem

at the moment, which would cause this problem. Mark On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp

Re: [gmx-users] parameters problem

for directive atomtypes Please help me rectify the problem of the order getting violated although same worked for topology generated by PRODRG. Thanks in advance. On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I

[gmx-users] antiparallel beta sheet

Dear users, I would like to analyse the time variation of antiparallel beta sheet formation. I am aware that dssp and stride program can calculate the beta sheet content but is there a tool that can distinguish between antiparallel and parallel beta sheet (in terms of giving numeric value as

[gmx-users] xpm2ps

Hello, I would like to change the scale of x axis and y axis of my dssp.eps file by different amounts. Example with xpm2ps -skip command I can write out every nr-th row and nr-th column but I want every nr-th row and mr-th column. Please suggest if it is possible to do so. Thanks in advance.

[gmx-users] parameters problem

Dear all I am trying to simulate a protein in 3 steps: energy minimization (using em.mdp), position restraints (using pr.mdp) and final production run by NPT ensemble (using full.mdp) at 300K At this temperature, it is known by previous literature survey that protein keeps its secondary