[gmx-users] Choosing terminals with AMBER ff

Hi everyone, I am considering selecting specific terminal caps, i.e. neutral N-terminal, charged C-terminal, with AMBER forcefield. However, there does not seem such an option. I ran "gmx pdb2gmx -f protein.pdb -o protein.gro -p protein.top -i protein.itp -ter -ignh". After selecting

Re: [gmx-users] Cut-off radius larger than the box length for Deform option?

Any help will be greatly appreciated. Surya Prakash Tiwari On Thu, Nov 2, 2017 at 5:05 PM, Surya Prakash Tiwari wrote: > Dear Gromacs users, > > Why simulation doesn't crash when one of the box length gets smaller than > the 2*cut-off radius mentioned in the MDP file, while

Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

On Mon, Nov 06, 2017 at 04:41:08PM -0800, Guyen Gn wrote: > Getting back to this thread after a while, is this the name of package?: > rpmdevtools.noarch 8.3-5.el7 Server > Red Hat Enterprise Linux Server release 7.3 (Maipo) > > I see it is included in the

Re: [gmx-users] water molecule cannot be settled during minimization!!!!

On Mon, Nov 6, 2017 at 12:17 AM, Seera Suryanarayana wrote: > Dear gromacs users > > I am trying to simulate one protein with 180 residues. During energy > minimization I got the falling error. > > Fatal error: > > step 26: Water molecule starting at atom 28787 can not be

Re: [gmx-users] water molecule cannot be settled during minimization!!!!

Investigate same water molecule mentioned in error in vmd or such program likely it is in close contact to other molecule.You can move it manually by altering coordinates in gro text file into more realistic starting position.Or probably even better if you redo your solvatation again (with

Re: [gmx-users] Water molecule error

Check the detail at following URL http://www.gromacs.org/Documentation/Errors On 7 Nov. 2017 8:12 pm, "Souparno Adhikary" wrote: > Hi, > > I was encountering an error as the following when running the production > simulation of a protein-membrane system. > > *> the

[gmx-users] Gmx minimdist

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear gmx users I am trying to analyz the minimum distance between periodic images,l and need to use  the .xtc file without

[gmx-users] Water molecule error

Hi, I was encountering an error as the following when running the production simulation of a protein-membrane system. *> the cut-off length is longer than half the shortest box vector or longer *>* than the smallest box diagonal element. Increase the box size or *>* decrease rlist.* I increased