[gmx-users] RE: How to freeze the atoms?

[Vitaly V. Chaban]

You can change integrator back to l-bfgs and the requested atoms will be
non-movable as well. MD in the file is just because I ran EM first and then
MD to check the problem. So, the last keyword is present.

What kind of calculation do you want to perform at all? - It's even better
to run MD for some time to relax the system completely.

-- 
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698


Hi
>
>
>
> I performed EM with all your input files and got the same results as you
> did(Gromacs-3.3.3). The C and O in carbonyl groups are nonmovable. The only
> difference between your
>
>
>
> and my mdp file is the "intergrator". It is "md" in yours and "l-bfgs" in
> mine. In Groamcs manual, "1-bfg" method is used for EM. I want to know
> whether "md" can be used for
>
>
>
> EM. I will perform EM in Gromacs-4.0.5 lately.
>
>
>
> Thank you for your time and patience!
>
>
>
> ; RUN CONTROL PARAMETERS
> integrator               = md
> ; Start time and timestep in ps
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 2000
> ; For exact run continuation or redoing part of a run
> init_step                = 0
> ; mode for center of mass motion removal
> comm-mode                = Linear
> ; number of steps for center of mass motion removal
> nstcomm                  = 1
> ; group(s) for center of mass motion removal
> comm-grps                =
>
>
> ----- 原始邮件 -----
> 发件人：Vitaly V. Chaban <vvchaban at gmail.com>
> 收件人：toby10222224 at sina.com, gmx-users at gromacs.org
> 主题：Re: 回复：Re: 回复：Re: How to freeze the atoms?
> 日期：2009-7-4 17:13:43
>
>
> Hi,
>
> First of all I suggest you to upgrade to the current version.
>
> In the next email I also attach all the files I used for a test run of your
> system.
>
> ~Vitaly
>
>
> 2009/7/4 <toby10222224 at sina.com>
>
>> Gromacs 3.3.3, there is no warning when I use shake with EM.
>> ----- 原始邮件 -----
>> 发件人：Vitaly V. Chaban <vvchaban at gmail.com>
>> 收件人：toby10222224 at sina.com, gmx-users at gromacs.org
>> 主题：Re: 回复：Re: How to freeze the atoms?
>> 日期：2009-7-4 13:47:47
>>
>>
>> What gromacs version do you use for now? The new version should warn you
>> that shake is impossible with EM.
>>
>> ~ Vitaly
>>
>>
>>
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