[gmx-users] Join my network on LinkedIn

LinkedIn Yi Gao requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Yi Accept invitation from Yi Gao http://www.linkedin.com/e/-85v1n9-hcsylp

Re: [gmx-users] parallel run problem for nwall

Gromacs is running well on multi-nodes without nwall. But with nwall, it doesn't work. Yi On Thu, Sep 9, 2010 at 9:28 PM, Mark Abraham wrote: > > > - Original Message ----- > From: Yi Gao > Date: Friday, September 10, 2010 12:23 > Subject: [gmx-users] parallel run prob

[gmx-users] parallel run problem for nwall

Dear Sir, I am using nwall to run my system. My version is Gromacs 4.0.7. Interestingly, I could parallel run my system on 1 node with 4 or 8 cpus, but when I run it on multi-node PC-cluster, it always fails and gives no message at all. I wonder if you could help me to resolve this problem? Thanks

Re: [gmx-users] x2top problem of dealing with spc216 water

Thanks a lot! On Sat, Sep 4, 2010 at 2:57 PM, Justin A. Lemkul wrote: > > > Yi Gao wrote: > >> And I have ~1500 spc water. Do I only need to add #include "spc.itp" in >> your topology? Thanks! >> >> > > I will reiterate the advice in my previo

Re: [gmx-users] x2top problem of dealing with spc216 water

And I have ~1500 spc water. Do I only need to add #include "spc.itp" in your topology? Thanks! Yi On Sat, Sep 4, 2010 at 2:53 PM, Yi Gao wrote: > Hi, Justin, > > Thanks for your advice! Do I need to add this part: > > #ifdef POSRES_WATER > ; Position res

Re: [gmx-users] x2top problem of dealing with spc216 water

"ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols SOL 216 Thanks a lot! Yi On Sat, Sep 4, 2010 at 11:21 AM, Justin A. Lemkul wrote: > > > Yi Gao wrote: > >> Hi, I used x2top to generate spc216.top. The spc216.gro file comes from >&

[gmx-users] x2top problem of dealing with spc216 water

Hi, I used x2top to generate spc216.top. The spc216.gro file comes from Gromacs tutor directory. I use Gromacs 4.0.5 version. The command line is x2top -f scp216.gro -o scp216.top. The error message is Can not find forcefield for atom OW-1 with 2 bonds Can not find forcefield for atom OW-4 with 2