[gmx-users] Suggestion on Umbrella sampling and peptide synthesis

Dear Friends, I want the suggestion from you on my plan of work. The plan is as follow : I have the protein pdb file in which two protein interact with each other and the dimer formed. The dimer is responsible for various bad effect in cell. So my aim is to to inhibit the dimer

[gmx-users] Suggestion on Umbrella sampling and peptide design

Dear Friends, I want the suggestion from you on my plan of work. The plan is as follow : I have the protein pdb file in which two protein interact with each other and the dimer formed. The dimer is responsible for various bad effect in cell. So my aim is to to inhibit the dimer

Re: [gmx-users] Invalid order for directive bondtypes

You probably need to define [atomtypes] before you can define [bondtypes] that use them. So swap the order of your #include statements. Mark On Mon, Oct 6, 2014 at 6:18 AM, Atila Petrosian atila.petros...@gmail.com wrote: Dear gromacs users I want to do MD simulation of a CNT. I used

Re: [gmx-users] Why should I repeat my simulation?

And one trivial coin from me... Not only the random seed for the initial velocity distribution must be altered, but it is also very good to start from a significantly different set of coordinates. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Sat, Oct 4, 2014 at 11:15 PM, fatemeh ramezani

Re: [gmx-users] constraint and restraints

Dear Tsjerk, Thank you very much. You are always ready to help. I have understood and taken your note : Whether it makes sense is another question. The dynamics is usually coupled throughout the protein. With very best regards, Niyaz - Original Message - From: Tsjerk

[gmx-users] Lithium Ions in Gromos53A6

Dear All, I find myself requiring lithium ions in a simulation using (a variant of) the Gromos53A6 forcefield. Chaging forcefields is not an appealing proposition due to the time already invested in the current one, so I was wondering had any suggestions or has perhaps gone to the effort of

[gmx-users] do_dssp

hi GMX  usersi use gromacs4.6.5  for protein-ligand complex simulationi wasn to study second structure of my protein for 20ns simulation. i used DSSP . I copied dssp file in /local/usr/bin and use following commandschmod +x dssp./dsspwhen i use following command:do_dssp -f md.xtc -s md.tpr -o

[gmx-users] Invalid order for directive bondtypes

Dear Mark Very thanks for you reply. I solved previous problem by swapping the order of my #include statements in forcefield.itp file. I used grompp for energy minimization, I obtained em.tpr file without any problem. Then I used mdrun for energy minimization, this step was done without error,

[gmx-users] Invalid order for directive bondtypes

my em.mdp file is as follows: integrator = steep nsteps = 5 nstcomm = 1 emtol= 10 emstep = 0.01 ns_type = grid rlist= 0.8 coulombtype = cut-off vdwtype

[gmx-users] can not split pdb beyond 1019

Hi All, I am trying to split my trajectory in single frame pdbs for some analysis using trjconv but it ends with an error after ouput 1019 pdbs. I tried with different version of gromacs (4.6.3 and 5.0) its the same error. trjconv -s ../em.tpr -f ../image_fitted.trr -o test.pdb -split 10 -b

Re: [gmx-users] Invalid order for directive bondtypes

On Oct 6, 2014 3:57 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Mark Very thanks for you reply. I solved previous problem by swapping the order of my #include statements in forcefield.itp file. I used grompp for energy minimization, I obtained em.tpr file without any

Re: [gmx-users] constraint and restraints

Hi Niyaz, In pymol you can try this (assuming your proteins are called proteinA and proteinB): import numpy d = numpy.array(cmd.get_model(proteinA).get_coord_list()) d -= numpy.array(cmd.get_model(proteinB).get_coord_list()) d = (d**2).sum(axis=1).tolist() tmp = list(d) alter proteinA,

Re: [gmx-users] can not split pdb beyond 1019

Hi, Thanks, good report. Unfortunately, someone in prehistoric times implemented the functionality common to -sep and -split using the or operator... everywhere except closing the file. So -split will continue opening files until it runs out of file handles (so later on, files can't be opened),

[gmx-users] NVE Energy drop in Mixed Precision 4.6.7

Hi. The system has 9000 water and a ~160 aa amino acid and uses amber99SB-ildn. After extensive NPT (300ns, 2ns ts), and then NVT equilibrium (300 ns, 2ns ts), the NVE simulation still has energy drop, despite of the very small time step. Is double precision gromacs the only solution? The mdp

[gmx-users] Polarisable (hydronium and hydroxide) model compatible with graphene?

Dear All,Until now, I have tried using TIPS3P and SWM4-NDP water models, to which I am unsuccessful in modelling water+ions on graphene.The nature of my research topic requires a charged model, which means using polarisable force field is most probably the best option.Could anyone recommend a