[gmx-users] Non standard or modified amino acids

Hello all I am doing a protein peptide MD. Can anyone suggest how to obatin topology file for modified peptides or non-standard amino acids? Best Wishes Suniba Sent from my iPhone -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Non standard or modified amino acids

On 12/22/15 9:49 AM, sun wrote: Hello all I am doing a protein peptide MD. Can anyone suggest how to obatin topology file for modified peptides or non-standard amino acids? Parametrize them according to whatever methods are required by the parent force field. Most modified amino acids

[gmx-users] meaning of -fr in trjconv

Hi all, I just want to know the meaning of "-fr" in trjconv program. Does that mean the number of certain frames? If so, what's the format of that? Merry Xmas in advance! -- Sincerely, Mr. Meng Zhenyu Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences

Re: [gmx-users] Extending simulations

sorry with my question is it true that for extending simulation use the following code? gmx grompp -f md.mdp -c md.gro -t md.trr -p topol.top -o md2.tpr gmx mdrun -deffnm md2 *md.gro and md.trr is files for first run On 12/22/15, Justin Lemkul wrote: > > > On 12/21/15 7:00

[gmx-users] high temperature molecular dynamics

Hi to all is there any guide for high temperature molecular dynamics simulation? i want to use this method for unfolding process. thank for your respond :-) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] high temperature molecular dynamics

tnx dear David On 12/22/15, David van der Spoel wrote: > On 22/12/15 10:58, masoud keramati wrote: >> Hi to all >> >> is there any guide for high temperature molecular dynamics simulation? >> i want to use this method for unfolding process. >> >> thank for your respond :-)

Re: [gmx-users] high temperature molecular dynamics

On 22/12/15 10:58, masoud keramati wrote: Hi to all is there any guide for high temperature molecular dynamics simulation? i want to use this method for unfolding process. thank for your respond :-) Just increase the temperature. You may need to reduce the time step though. -- David van

Re: [gmx-users] Extending simulations

Hi I think it should be like this: tpbconv -s previous.tpr -extend timetoextendby -o new.tpr mdrun -s new.tpr -cpi previous.cpt On Tue, Dec 22, 2015 at 2:07 PM, Mark Abraham wrote: > Hi, > > Please start with >

[gmx-users] How to calculate which residues are within a certain distance from a carbon nanotube

Hello, I am simulating a single stranded DNA molecule in the presence of an armchair carbon nanotube using GROMACS 4.5.6. One of the reviewers of the paper has asked to calculate the numbers of nucleic acid bases are stacked to the CNT surface as a function of simulation time as well as

Re: [gmx-users] How to calculate which residues are within a certain distance from a carbon nanotube

On 12/22/15 4:25 AM, soumadwip ghosh wrote: Hello, I am simulating a single stranded DNA molecule in the presence of an armchair carbon nanotube using GROMACS 4.5.6. One of the reviewers of the paper has asked to calculate the numbers of nucleic acid bases are stacked to the CNT