Re: [gmx-users] genbox + python bug?

Thanks for the insights, Mark. It was a 'aprun' issue. When I remove it from the command, everything worked out. -- Marcelo 2015-03-13 14:10 GMT-03:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hey, I have a

Re: [gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch

Thanks David for the clarifications. I really appreciate it.Atanu On Friday, 13 March 2015 2:07 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2015-03-13 00:30, atanu das wrote: Hi David, I have checked both the codes, g_angle.c and g_chi.c, and the same Cos function is

Re: [gmx-users] genbox + python bug?

On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hey, I have a python script running gmx commands (version 4.6.7) until the following: *if systype == 'system_1' or systype == 'system_2':genboxcommand = aprun -n 1 genbox_mpi -cs spc216.gro -cp + prefix +

[gmx-users] diisopropylethylene topology

Dear All, Does anyone has the itp file for diisopropylethylene? It would be very helpful if you can share. Many thanks in advance. Regards, Quy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Placing system at the centre of the box.

Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of epoxide group on one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. I used the following commands to

Re: [gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch

On 2015-03-13 00:30, atanu das wrote: Hi David, I have checked both the codes, g_angle.c and g_chi.c, and the same Cos function is used in both the cases (please correct me if I am wrong). g_angle analysis: I have used the following command to calculate the average autocorrelation function

Re: [gmx-users] boron atom

OK, thanks Justin. Best regards On Fri, Mar 13, 2015 at 1:52 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/12/15 9:16 AM, Faezeh Pousaneh wrote: Hi, Does any one know which force filed contains 'Boron' atom? I need it for my simulation, molecule sodium tetraphenylborate. None of

[gmx-users] problem in defining protonation state of amino acids

Hi everyone, I want to do a constant pH simulation of my protein using CHARMM36. I calculated protonation state of various amino acid at required pH using H++ server. However when trying to run pdb2gmx got fatal error Atom HB3 in residue SER 3 was not found in rtp entry SER with 11 atoms while

[gmx-users] query regarding coarse grained simulation of a peripheral membrane protein

​Hi, How do i generate a topology file of a peripherally attached dimeric protein with a homogenous lipid bilayer using coarse grained approach? ​i have concatenated the coarse grained structure of lipids and protein prior to this. -- *Best,* *Antara* -- J.R.F.(Project) Systems Biology Group

Re: [gmx-users] problem in defining protonation state of amino acids

On 3/13/15 8:08 AM, Tushar Ranjan Moharana wrote: Hi everyone, I want to do a constant pH simulation of my protein using CHARMM36. I Just for clarity fixed protonation and constant pH are not synonymous. Natively, GROMACS does not do constant pH simulations, though I believe some groups

[gmx-users] genbox + python bug?

Hey, I have a python script running gmx commands (version 4.6.7) until the following: *if systype == 'system_1' or systype == 'system_2':genboxcommand = aprun -n 1 genbox_mpi -cs spc216.gro -cp + prefix + .min0.gro -p + prefix + .top -o + prefix + .wat.gro -maxsol + str(water+ion) +