[gmx-users] question

Dear Tsjerk I used pdb2gmx -f be_near.pdb -ignh -merge Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscri

Re: [gmx-users] energy minimization error

Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? Cheers James On Sun, May 17, 2015 at 9:02 AM, Justin Lemkul wrote: > > > On 5/16/15 6:27 AM, James Lord wrote: > >> Dear gmx users, >> I am getting this error,

Re: [gmx-users] energy minimization problem

On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Th

Re: [gmx-users] position restraints

On 5/16/15 8:13 AM, Ming Tang wrote: Dear all, I want to minimize my system to relax the solvent with the positions of heavy atoms within the protein restrained. I searched the archives and got the idea that I need to put something like this in topology: #ifdef POSRES_WATER ; Position restr

Re: [gmx-users] energy minimization error

On 5/16/15 6:27 AM, James Lord wrote: Dear gmx users, I am getting this error, Can anyone help me to get around this? Cheers James Program mdrun, VERSION 4.6.3 Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 8 nodes

Re: [gmx-users] warnings in energy minimization

On 5/16/15 12:14 AM, James Lord wrote: Hi all, I am using Justin's minim.mdp to energy minimize my system and I am getting these warnings,Should I care about them? It is saying that my simulation may not be stable? Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps

Re: [gmx-users] question

Hi Andrew, Can you post the exact pdb2gmx command line you use? Cheers, Tsjerk On Sat, May 16, 2015 at 10:13 PM, Andrew Bostick wrote: > Dear Tsjerk > > residue numbers in chain B are as 220-434. > GLU residue is 380. > > residue numbers in chain E are as 435-551. > LYS residue is 540. > > Ho

[gmx-users] question

Dear Tsjerk residue numbers in chain B are as 220-434. GLU residue is 380. residue numbers in chain E are as 435-551. LYS residue is 540. How to merge these two chains through these two residues? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Maili

[gmx-users] question

Dear Tsjerk Thanks for your quick answer. Yes, I want to have a link between two chains (GLU from chain B and LYS from chain E). I am using gromacs 4.5.3. Can I use the option -merge in this version? After using -merge with pdb2gmx, I encountered with: Invalid command line argument: -merge How

Re: [gmx-users] question

Hi Andrew, I guess you want a link between the chains. In that case you'll need to use the option -merge. Cheers, Tsjerk On Sat, May 16, 2015 at 8:46 PM, Andrew Bostick wrote: > After using pdb2gmx, my terminal output is as follows: > > Using the Gromos43a1 force field in directory gromos43a1

[gmx-users] question

After using pdb2gmx, my terminal output is as follows: Using the Gromos43a1 force field in directory gromos43a1.ff Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/watermodels.dat Select the Water Model: 1: SPCsimple point charge, recommended 2: SPC/E extended s

[gmx-users] question

Dear Justin In pdb file, I corrected the distance between the two residues I want bonded together to form the isopeptide bond (within 10% of my criterion (0.13 nm). The new distance is 0.128 nm. I used following specbond.dat, residuetyps.dat and aminoacids.rtp files.

Re: [gmx-users] energy minimization problem

Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after run

[gmx-users] position restraints

Dear all, I want to minimize my system to relax the solvent with the positions of heavy atoms within the protein restrained. I searched the archives and got the idea that I need to put something like this in topology: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_res

[gmx-users] energy minimization error

Dear gmx users, I am getting this error, Can anyone help me to get around this? Cheers James Program mdrun, VERSION 4.6.3 Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and

[gmx-users] (no subject)

Hi dears Our team want to buy a computer for MD Runs (Gromacs). We are not high in budget. Our solution is as following: CPU: 2x Intel Xeon Processor E5-2697 v3GPU: 3x NVIDIA GeForce GTX 980 (GIGABYTE - NVIDIA GeForce GTX 980 3-way SLI Gaming + water cooling system)MB: ASUS-Z10PE-D8 WS or GIGABY