RE: [gmx-users] Restart Replica Exchange

Hi, In gromacs 4.0 the checkpoint files of the different replicas might not be in sync (written at the same step). In that case you will have to use tpbconv with the trajectory of each replica and select the last common frame. In the 4.5 release I fixed this issue by synchronizing the checkpoi

Re: [gmx-users] Restart Replica Exchange

Hello, U can generate the restart files for last common frame in all your trajectory and use the same for continuing the simulation . On Sat, Sep 4, 2010 at 3:16 PM, Berk Hess wrote: > Hi, > > In gromacs 4.0 the checkpoint files of the different replicas might not be > in sync (written at the

[gmx-users] salt bridge

Hi I want to see specific salt bridge residues for example which Arg by Glu is in salt bridges. But in step we got a list pairs in which Cl ions (Cl ions added to neutralize peptide in solvent by genion) are paired to residues. I don't know what is the problem and how can I have salt bridge residue

Re: [gmx-users] salt bridge

shiva birgani wrote: Hi I want to see specific salt bridge residues for example which Arg by Glu is in salt bridges. But in step we got a list pairs in which Cl ions (Cl ions added to neutralize peptide in solvent by genion) are paired to residues. I don't know what is the problem and how ca

[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

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

Yi Gao wrote: 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 f

[gmx-users] about Rg

Hello Justin, Now I am using g_polystat for calculating Rg. However results are pretty similar to those obtained from g_gyrate. The command line I am using is g_polystat -f *.trr -s *.tpr -o polystat-mw -n *.ndx -mw -xvgr -w - I noticed -mw option does not change Rg. Also When I choose all chai

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

Hi, Justin, Thanks for your advice! Do I need to add this part: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.it

Re: [gmx-users] about Rg

Moeed wrote: Hello Justin, Now I am using g_polystat for calculating Rg. However results are pretty similar to those obtained from g_gyrate. The command line I am using is g_polystat -f *.trr -s *.tpr -o polystat-mw -n *.ndx -mw -xvgr -w - I noticed -mw option does not change Rg. Also Whe

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 restraint for each water oxygen > [ position

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

Yi Gao wrote: Hi, Justin, Thanks for your advice! Do I need to add this part: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif This section is only necessary

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

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 previous message - do some tutorial material on a simple system, read Chapter 5, then proceed. -Justin Yi On Sat, Sep 4, 2010 at 2:53 PM, Yi G

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 previous message - do some tutorial > material on a simple

[gmx-users] Re: 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 O

[gmx-users] g_polystat

Hello Justin, I have read help of the command I am using several times. My understanding is that g_polystat calculates Rg of 8 chains and takes the average if no specific index groups are selected. Below are the groups I have created for 8 chains. g_polystat -f *.trr -s *.tpr -o polystat-mw-xvgr-8

Re: [gmx-users] g_polystat

Moeed wrote: Hello Justin, I have read help of the command I am using several times. My understanding is that g_polystat calculates Rg of 8 chains and takes the average if no specific index groups are selected. Below are the groups I have created for 8 chains. g_polystat -f *.trr -s *.tpr -

[gmx-users] Tables and forcefield parameters

Hi, ques1: I have 3 energy groups. I am interested in using tables for LJ and coulomb interactions for Group1-group2 interactions. For all other interactions: 1) Group1-group1 -all interactions-bonded and non-bonded 2) Group2-group2 -all interactions -bonded and non-bonded 3) All possible combina