[gmx-users] DANGLING BOND IN GOLD-PROTEIN SIMULATION

regards, Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe

[gmx-users] au virtual site

Dear gromacs users  I want to simulate gold nanoparticle by golp force field that needs to determine virtual sites for Au atoms. I read gromacs manual section 5.2.2 and 4.7 but it is not clear that how can I do it and .also I read virtual site tutorial for CO2 but it is for a 3 atomic molecule

[gmx-users] au virtual atom

to manually sort atoms and consider for every group a virtual site? thanks ramezani Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

[gmx-users] AU-S bonded parameter

multiple this K to sigma(au-s) and then put in bonded file? thank you   Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please

[gmx-users] gold-protein simulation stop by error in equilibrum step

em1.mdp, em2.mdp,em3.mdp, md100.mdp(temperature=100 k),md200.mdp(temperature=200k) and after these steps I do main simulation in 300k. I attached all mdp file. in md100.mdp steps, mdrun stops in middle of running and appear above error. please help me to resolve my problem thank you Fatemeh

[gmx-users] gold-S simulation

can but my system doesn't work. please help me   Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un

Re: [gmx-users] gold-S simulation

Dear francesco I extract gold parameter from papers that I attached them for you. But  for gold and other atom parameters, you should calculate them using common combination rule. Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] gold-S simulation

hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you.   Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] Re: gmx-users Digest, Vol 104, Issue 73

gold and sulfur? What do you suggest? How do I define for the program that can be established between these two atoms covalent bond ? many thanks Fatemeh Ramezani From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org

[gmx-users] Re: gmx-users Digest, Vol 104, Issue 83

in ffnonbonded file? thank you Fatemeh Ramezani From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Tuesday, 18 December 2012, 14:30 Subject: gmx-users Digest, Vol 104, Issue 83 Send gmx-users mailing list submissions

[gmx-users] Re: gold-protein simulation

for this closing?Is not it true that when there is no epsilon and Sygma between two atoms, should not be move toward one another?   Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

[gmx-users] (no subject)

? (Of course, the whole system charge that is shown in  the first grompp step is very low near -0.11). Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support

[gmx-users] separate equilibrium

simulation of  them. How can I do this? Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests

[gmx-users] au--protein separate equilibration

    = Y Y Y Y Y Y comm_mode = None Are these .mdp file right? Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

Fw: [gmx-users] au--protein separate equilibration

Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that I freeze AU atoms in it,

[gmx-users] au-protein separate minimization

Dr. Justin I want to do energy minimization of AU and Protein in separate steps and in last emails you said a way for this, is freezing of them. Then I decide to freeze AU and minimize Protein and in next step vise versa. I'm wrong? Fatemeh Ramezani -- gmx-users mailing listgmx-users

[gmx-users] au-protein simulation, water constraint_algorithm

be selected in the topology, means that with the above settings in md.mdp file, should I add [  settles  ] ;  OW    funct  doh dhh 1 1 0.1 0.16333 in .top file? Are these settings correct? If that is the constraint = none, constraint_algorithm = lincs applies? many thanks Fatemeh

[gmx-users] bonding energy

between two molecules? thank you Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests

[gmx-users] can I change atom position after x steps

Dear all  I am simulating gold nanoparticle interaction with 10 aminoacids.Two amino acids have been far from the nanoparticleafter 2000 steps. Now, Can I change after2000 steps, the position of these 2 aminoacids in  PDP file and then continue the simulation? Fatemeh Ramezani -- gmx-users

Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology

the command that I used is :  g_energy    -f  md300.edr   -s  fws_md300.tpr    -o energy.xvg    -pairs pairs.xvg  Fatemeh Ramezani From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users

Re:Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology

 Dear Justin I thought by use of  -pairs I can calculate energy between any 2 groups from index file. when I use g_energy, result is a .xvg file that shows energy of system but I need to calculate energy between specific groups. is there any way for me?   thanks Fatemeh Ramezani -- gmx

[gmx-users] interaction energy

energy is equal to the van der Waals energy? Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe

[gmx-users] fattyn acid parameter in OPLSAA forcefield

 Hi all I want to simulate protein-fatty acid-AU complexs by OPLSAA force field.  But OPLSAA force field, hasn't any parameter for fatty acid. Can I use CHARMM fatty acid parameters in OPLSAA force field? Anyone has better suggestion? Fatemeh Ramezani -- gmx-users mailing listgmx

[gmx-users] acidic pH

Hello dear users I'm simulating gold nanoparticle interaction with protein. I want to change the pH of system. What would  need to be changed to simulate this system at pH 3.0? thanks you   Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] AMINOACIDS

 Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? Thank you Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

Fw: [gmx-users] AMINOACIDS

 Dear Justin I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid  deprotonate? and if pKa of  aminoacids is bigger thanmy desired pH, I must protonate this amino acid? Thank you Fatemeh Ramezani

[gmx-users] aminoacids protonation in different ph

 Dear Justin I found a server : http://biophysics.cs.vt.edu/ that protonate aminoacids according to desired pH easily. Sincerely Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] protein unfolding in water

of nanoparticle. I think there is a problem. What is the solution you offer me? What is the problem? sincerely Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support

[gmx-users] forcefield and setting

=  yes gen_temp    =  300.0 gen_seed    =  173529 energygrps  = Protein  Sol Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support

[gmx-users] ensemble selection

should be done by NVT and NPT and then MD should be done with NPT ensemble. in your idea should I repeat my MD run by NPT ensemble? what is the difference of my result  between this two? thank you Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman