[gmx-users] problem with angle restraints

I trying to use angle restrain for an ligand molecule. I have included the following information in my .itp file of the ligand - [ angle_restraints ] ; aiajak functc0c1c2c3 6 1 7 1 106.9510001

Re: [gmx-users] Frozen N2 in a very long tube

- Original Message - From: shuai shuai bansh...@gmail.com Date: Saturday, July 10, 2010 2:27 Subject: [gmx-users] Frozen N2 in a very long tube To: gmx-users@gromacs.org Hear all, Recently I met a strong error from gromacs. Therefore I would like to know whether you have

[gmx-users] Re: the Pressure control in GROMACS 4.0.7

Dear users,  I think the pressure control in gromacs 4.0.7 may have some problems. First ,The pressure value fluctuates widely ,even between -7984.377930 and 5920.053711 bar.Second,the average pressure sometimes is much larger than what I have set,for example, I have set ref_p  = 1.0 , but

[gmx-users] Re: Frozen N2 in a very long tube

Dear Shuai: Please try to couple temperature for nanotube and nitrogen separately. BTW, what is your partial charge and how did you construct it? Good luck! Dr. Vitaly Chaban Recently I met a strong error from gromacs. Therefore I would like to know whether you have experienced the same

Re: [gmx-users] Re: the Pressure control in GROMACS 4.0.7

On 2010-07-10 09.47, Vitaly Chaban wrote: Dear users, I think the pressure control in gromacs 4.0.7 may have some problems. First ,The pressure valuefluctuates widely ,even between -7984.377930 and 5920.053711 bar.Second,the average pressuresometimes is much larger than what I have set,for

Re: [gmx-users] Installing gromacs from git

Hi, if you configure the git version without the --enable-mpi flag, it will turn on threads by default. Depending on the number of processors you have on your workstation, it will then use these many threads. You can disable that with mdrun -nt 1 ... Carsten On Jul 10, 2010, at 1:57 AM, Sai

[gmx-users] Re: Pressure control in GROMACS 4.0.7

Dear Professor van der Spoel: Don't you have an idea why the average value of pressure appears to be (always?) slightly larger and (never?) smaller than requested one? I did not collect the statistics systematically but I often mentioned this curious fact. Vitaly fluctuations are

Re: [gmx-users] Re: Pressure control in GROMACS 4.0.7

On 2010-07-10 12.40, Vitaly Chaban wrote: Dear Professor van der Spoel: Don't you have an idea why the average value of pressure appears to be (always?) slightly larger and (never?) smaller than requested one? I did not collect the statistics systematically but I often mentioned this curious

[gmx-users] Re: the Pressure control in GROMACS 4.0.7

Dear users:   I am simulating a CNT in water. In the energy minimization step, I   restrain the CNT by a constant 10e8,because I don't want the CNT to deform. After minimization,the energy is -44054.835938. Then NVT and NPT equilibration , at this step,the end C atoms are fixed by a constant

Re: [gmx-users] Re: the Pressure control in GROMACS 4.0.7

On 2010-07-10 15.56, zhongjin wrote: Dear users: I am simulating a CNT in water. In the energy minimization step, I restrain the CNT by a constant 10e8,because I don't want the CNT to deform. After minimization,the energy is -44054.835938. Then NVT and NPT equilibration , at this step,the end C

Re: [gmx-users] Re: Frozen N2 in a very long tube

Dear all, thanks for your suggestions. During this NVT simulation, I keep nanotube rigid. So the temperature should only couple to Nitrogen instead of the whole system as my original input file. I will try to couple temperature only to nitrogen to see whether this is the reason. Many thanks

RE: [gmx-users] pdb2gmx with DNA

Hi Thanks, I thought so too. My command line is: pdb2gmx -f xxx.pdb file The -ter flag is set to default, i.e. charged termini. When I use the -ter flag for interactive termini selection and I select NONE for both N- and C-ter the message becomes: Program pdb2gmx, VERSION

Re: [gmx-users] Re: Frozen N2 in a very long tube

shuai shuai wrote: Dear all, thanks for your suggestions. During this NVT simulation, I keep nanotube rigid. So the temperature should only couple to Nitrogen instead of the whole system as my original input file. I will try to couple temperature only to nitrogen to see whether this is the

Re: [gmx-users] pdb2gmx with DNA

I think there have been changes to the way pdb2gmx handles termini, perhaps related to the impending inclusion of the ffamber ports, but I do not know. I worked with someone else with this issue, and it was solved by renaming residues, which seems like a terrible solution. I guess your DNA

[gmx-users] Treating nonbondend interactions in GROMACS

Hello Justin, Thanks for your comments and also I really liked your reasoning for getting no answer from people that are not awake : You are right ;) Actually, I have no charged particles in my system. All I have is carbon and hydrogen. I read through the manual meticulously about nonbonded

Re: [gmx-users] Treating nonbondend interactions in GROMACS

jojo J wrote: Hello Justin, Thanks for your comments and also I really liked your reasoning for getting no answer from people that are not awake : You are right ;) Actually, I have no charged particles in my system. All I have is carbon and hydrogen. I read through the manual