[gmx-users] a box of water

Hi all, I want to do Molecular dynamics simulation of a box of water (SPC type). I get the spc216.pdb file from the gromacs/share/tutor. Firstly, I did geometry optimization for nsteps= 5. Now, can I continue with production run or do I need to do equilibration runs to arrive correct

Re: [gmx-users] a box of water

Thanks a lot for your quick reply Justin. I got it. Turgay 2012/9/7 Justin Lemkul jalem...@vt.edu: On 9/7/12 7:34 AM, Turgay Cakmak wrote: Hi all, I want to do Molecular dynamics simulation of a box of water (SPC type). I get the spc216.pdb file from the gromacs/share/tutor. Firstly, I

[gmx-users] inquiry about SAS

Hi all, I am calculating SAS using g_sas of my system (several peptides in water and ions, Na and Cl). I choose: for calculation group: non-water for output group: protein (400 out of 750 atoms were classified as hydrophobic) When I plot the Area vs time graphs, both the

[gmx-users] number of contact

Dear all, Does the number of contact calculated by g_mindist mean that interaction between two groups? If so, could you kindly check the reliability of the case I have written below. I have 10 peptides (5 of them are X-peptide and 5 of them are Y-peptide) in a box filled with water. After MD

[gmx-users] eneconv with -dt flag

Hi all, I have encountered a problem using eneconv with -dt flag. I have several energy files. Firstly, I concatenated them using the following. eneconv -f first.edr second.edr -settime -o total.edr But, total.edr is so large. To reduce the size of file, I used the below command:

Re: [gmx-users] eneconv with -dt flag

Thanks Mark. I want to calculate Coulomb and Lennard-Jones energies using total_dt100.edr . But, I am not sure I can get the correct energies? Turgay 2012/6/8 Mark Abraham mark.abra...@anu.edu.au On 8/06/2012 10:40 PM, Turgay Cakmak wrote: Hi all, I have encountered a problem using

[gmx-users] Electrostatic interaction energy

starting the simulation. So in this case, is there any way to get this interaction energy OR can I just calculate the electrostatic energy of the whole system? Thanks in advance, Turgay 2012/6/8 Mark Abraham mark.abra...@anu.edu.au On 8/06/2012 11:51 PM, Turgay Cakmak wrote: Thanks Mark. I want

[gmx-users] dssp doubt

Hi all, I downloaded the original form of DSSP which is recently called DSSPold. Whenever I use the following: *do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm * It selects Protein by it-self without any control from me. I want to choose from the list, for example not protein but C-alpha. To

[gmx-users] hydrophobic contacts

Hi All, To be able to get information about the hydrophobic contacts, I prepared index.ndx which includes 2 groups of atoms that belong to hydrophobic residues of my system. Then, I used the command “g_dist -f traj.xtc -s topol.tpr -n index.ndx -dist 0.4 -lt -o lifetime.xvg” . which gave

[gmx-users] trajectory analysis

Hi all, I would like to get information about *pi-pi stacking*, *van der Waals*, *electrostatic and hydrophobic interactions* for my system (several-peptides in a box filled with water). Can Gromacs compute these interactions? As far as I see from mailing-list, to get information on

Re: [gmx-users] trajectory analysis

Thank you for your reply. I will read the manual more carefully. 2012/6/5 Justin A. Lemkul jalem...@vt.edu On 6/5/12 4:40 AM, Turgay Cakmak wrote: Hi all, I would like to get information about *pi-pi stacking*, *van der Waals*, *electrostatic and hydrophobic interactions* for my system

[gmx-users] Incomplete frame

Hi gromacs users, I concatenated 7 trajectory files (each one has 10ns simulation) using trajcat. Then, when I used gmxcheck, I get following error. Reading frame 0 time0.000 # Atoms 68393 Precision 0.001 (nm) Reading frame 13000 time 26000.000 *WARNING: Incomplete frame: nr 13739

Re: [gmx-users] Incomplete frame

AM, Turgay Cakmak wrote: Hi gromacs users, I concatenated 7 trajectory files (each one has 10ns simulation) using trajcat. Then, when I used gmxcheck, I get following error. Reading frame 0 time0.000 # Atoms 68393 Precision 0.001 (nm) Reading frame 13000 time 26000.000 *WARNING

[gmx-users] trjconv_snapshot

Hi Gromacs users, I have a problem getting a snapshots using trjconv. If you could help me, I would be very grateful. Below, I try to explain what I did and problem happened. Firstly, I have done 10ns long simulation (several peptides in a box). And then, using the outputs of that simulation

[gmx-users] trjconv_snapshot

Hi Rama, Thanks for your quick reply. Catenate two trajectory with help of trjcat -h to get snapshot of particular time use trjconv -dump time use appropriate pbc option I have also used trjconv with -dump and -pbc nojump options, but still I have same problem. you are using -b 1 -e 1

[gmx-users] extention of the simulation

Hi Gromacs users, I have a question related to the extension of the simulation. I have done 10 ns simulation (several peptides in a box). Now, I want to extend it 10ns more. - As far as I see from “Justin Lemkul’s Lysozyme in water tutorial”, to extend simulation, following should be

[gmx-users] multiple molecules in a box

Hi gromacs users, I have two different molecules, lets say A and B. I want to put 5 A molecules and 5 B molecules in the same box. I carried out the following steps. 1) For both A and B, I used *genbox* with *-nmol* flag separetely and obtained the A_multiple and the B_multiple structure

[gmx-users] (no subject)

Hi all, I am new to the Gromacs and just started to use Gromacs for MD simulations. I am tring to extend the simulation (protein in a box) 10 ns more. For this, I used the following command: grompp -f md.mdp -c md_first.gro -t md_first.cpt -p topol.top -o md_second.tpr mdrun It seems to run.. I