[gmx-users] h-bonds constraints

Hi I want to run an NPT simulation with all h-bonds constrained. How does grompp identify the Hydrogen atoms given that forcefield labels like HA, HC, HE are used. Is it the mass? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] regarding x2top

hello sir, thanks for your reply.. The thing is i seperated my fattyacid portion from aminoacid.. so carbon missing its bond. That 1st carbon linked to c, one double bonded o and glu aminoacid... how i need to model my input.. shall i need to draw my fattyacid portion alone in chemsketch and th

Re: [gmx-users] regarding x2top

priya thiyagarajan wrote: hello sir, thanks for your reply.. The thing is i seperated my fattyacid portion from aminoacid.. so carbon missing its bond. That 1st carbon linked to c, one double bonded o and glu aminoacid... how i need to model my input.. shall i need to draw my fattyacid p

[gmx-users] Metal Ion Position

Hi, I have a question on how to calculate the metal ion position in a protein in a simulation. To be more more specific, I would like to make sure the metal ion stay in the binding site throughout the simulation, and not sure which analysis function to use. I have tried g_rms, and did not work

Re: [gmx-users] Metal Ion Position

simon sham wrote: Hi, I have a question on how to calculate the metal ion position in a protein in a simulation. To be more more specific, I would like to make sure the metal ion stay in the binding site throughout the simulation, and not sure which analysis function to use. I have tried g

Re: [gmx-users] Regarding free energy calculation

Yes, changing the net charge of the system is something that is rather complicated in fact (one can plunge ahead and do it while ignoring the complications, but the results will typically be rather system-size dependent and essentially wrong). For more details refer to the Kastenholz and Hunenberge

[gmx-users] About restraint for umbrella sampling

Dear jusitn Thank you for your previous reply.   I am doing Umbrella sampling using plumed-gromacs. for that i have done umbrella pulling using gromacs only I have extracted the frame of reference from 120ps to 360ps . i am u

[gmx-users] Reg: Parallel run

Dear Users, I am trying to run my simulation in parallel using above 40 threads on a cluster using qsub system but i am getting the following errors Fatal error: The number of nodes you selected (43) contains a large prime factor 43. In most cases this will lead to bad performance. Choose a n

[gmx-users] regarding rtp file

hello sir, Thanks for your reply.. i like to know is it better to do x2top for my whole protein instead of seperating fattyacid from aminoacid to generate rtp file and top file since mine is a cyclicheptapeptide.. so that i can use that top file for doing my energy minimization ,position restr ad

Re: [gmx-users] regarding rtp file

priya thiyagarajan wrote: hello sir, Thanks for your reply.. i like to know is it better to do x2top for my whole protein instead of seperating fattyacid from aminoacid to generate rtp file and top file since mine is a cyclicheptapeptide.. so that i can use that top file for doing my energy

Re: [gmx-users] Reg: Parallel run

Rohit Farmer wrote: Dear Users, I am trying to run my simulation in parallel using above 40 threads on a cluster using qsub system but i am getting the following errors Fatal error: The number of nodes you selected (43) contains a large prime factor 43. In most cases this will lead to bad

[gmx-users] Help with g_density

Dear All I run g_density on a membrane protein. Here are the results   http://elisacarli.altervista.org/densityhead.jpg http://elisacarli.altervista.org/tailsDensity.jpg   Could you help me to give an interpretation to my analysis?   Thank in advance-- gmx-users mailing listgmx-users@gromacs.

RE: [gmx-users] Help with g_density

What is your interpretation? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is

[gmx-users] which may caused this error

Hi, I have very high frequency meeting below error: [hostname-c06:07555] *** Process received signal *** [hostname-c06:07555] Signal: Segmentation fault (11) [hostname-c06:07555] Signal code: Address not mapped (1) [hostname-c06:07555] Failing at address: 0x2aaab3248120 [hostname-c06:07555] [ 0]

Re: [gmx-users] which may caused this error

lina wrote: Hi, I have very high frequency meeting below error: [hostname-c06:07555] *** Process received signal *** [hostname-c06:07555] Signal: Segmentation fault (11) [hostname-c06:07555] Signal code: Address not mapped (1) [hostname-c06:07555] Failing at address: 0x2aaab3248120 [hostname-

[gmx-users] regarding topology

hello sir, Thanks for your reply. initially i tried with pdb2gmx command.but i got error. as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC. when i performed pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh it showed error as *Processing chain 2 'A' (16 atoms,

Re: [gmx-users] regarding topology

priya thiyagarajan wrote: hello sir, Thanks for your reply. initially i tried with pdb2gmx command.but i got error. as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC. when i performed pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh it showed error as *Proc

Re: [gmx-users] LINCS error

I get an error like this= Step 43230, time 86.46 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033583, max 1.621884 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.00.44

Re: [gmx-users] LINCS error

aiswarya pawar wrote: I get an error like this= Step 43230, time 86.46 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033583, max 1.621884 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length

Re: [gmx-users] Regarding free energy calculation

Thanks a lot for your suggestions. On Mon, Dec 19, 2011 at 21:00, David Mobley wrote: > Yes, changing the net charge of the system is something that is rather > complicated in fact (one can plunge ahead and do it while ignoring the > complications, but the results will typically be rather system