[gmx-users] solvent implicit error

Hi All I am trying analyze the dynamics of polymer of GlcN residues using ffG53a6 force field. I included in toplogy file the follow sentence: ;Include GB Parameters [ implicit_genborn_params ] #include "mypath/MYgbsa.itp" The MYgbsa.itp is : ; atype sar st pi gbr hct

[gmx-users] g_hbond solvent insertion problem

Hi all: I´m using gromacs version 4.0.2 and a box type truncated octahedron for the MD simulation. I need to analyze hydrogen bonds with solvent (water)insertion. I used the following command: g_hbond –f *.xtc –s *.tpr –n *.ndx –num num.xvg –dist *.xvg –ang *.xvg –a 45 –r 0.3 –ins. I selected accep

[gmx-users] intrinsic viscosity

Hi All: I am using Gromacs 4.0.2 for the MD simulation of carbohydrates and I am trying to compute the intrinsic viscosity of them. Can I have it whith same gromacs programs? Sameone has experience about this? Any help would be appreciated Carmen -- gmx-users mailing listgmx-users@gromacs.

Re: [gmx-users] [Fwd: Please solve my problem]

Hi again the MPI coding is OPEN MPI 1.2.7 that is found in the ROCKS CLUSTER 5.1 distribution thanks Carmen > > ceste...@unsl.edu.ar wrote: >> Hi All >> I have similar problem using gromacs 4.0.2. >> The MD simulation (5 ns) on single processor is complited in 5 days, but >> the same MD can`t be c

Re: [gmx-users] [Fwd: Please solve my problem]

Hi All I have similar problem using gromacs 4.0.2. The MD simulation (5 ns) on single processor is complited in 5 days, but the same MD can`t be complited on cluster on 4 or 8 processors. The MD simulation is stopped without any error message. Any help would be appreciated Carmen > > To, >D

Re: [gmx-users] new block lactitol

Hi Justin Thanks for your answer. I had check the relevant sugar, but I still have the problem of parameterization of the open GLC ring that forms the lactitol molecule. If you know of a similar example please let me know. Thanks very much Carmen > > ceste...@unsl.edu.ar wrote: >> Hi All >> I am tr

[gmx-users] new block lactitol

Hi All I am trying to analize the dynamics of polysaccharid which include lactitol grups (b-D-Galp-(1-4)-D-Glc-ol), using ffG53a6 force field. I need to make a new building block in .rtp file, but I don´t know about the proper parameters. Someone has made a lactitol´s block or can help me with the

[gmx-users] (no subject)

Hi all We are sorry to bother you on perhaps a simple question, but elusive to us. > We want to run a MD simulation of three units of chitosan (B(1-4)GlcN). > We are using Gromacs ffG53A6 force field and we can not find in the > corresponding library the charges corresponding to the NH2 group in >

[gmx-users] charge atoms

Hi All I am trying to analyze the dynamics of polymer of GlcN residues using ffG53a6 force field. I made a new building block in .rtp file, but I haven´t the charge of some atoms. Which is the best procedure to obtein new charges? Someone has experience about this? Any help would be appreciated Ca

Re: [gmx-users] problem with new sugar residue

Many thanks in advance,but the problem seems to be solved just by not including the new residue name in the aminoacids.dat file, despite the instruction to do so in sec.5.5.1 chapter 5 Topologies of the manual. Can you tell me if this procedure is correct? Thanks again Carmen > Hi Carmen, > > You r

[gmx-users] problem with new sugar residue

I added a new sugar residue in ffG53a6.rtp file, and I included in the aminaocid.dat file. I got the following problem using pdb2gmx : ... Program pdb2gmx, VERSION 3.3.2 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom O in r