Try a short run using pmemd and cpus. Perhaps the restraint energy is too
high.
On Fri, Aug 8, 2025, 8:09 AM Gourav Das <dgourav109.kgpian.iitkgp.ac.in>
wrote:
> Thank you Professor, for your valuable assistance. I have successfully run
> the umbrella sampling simulation using pmemd. However, when I am running
> with pmemd.cuda, I am getting the following error:
>
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> encountered
>
> I did not encounter such an error when defining dihedral with individual
> atoms. Could you kindly advise me on how to resolve this issue?
>
> Thank you!
>
> Sincerely,
> Gourav Das
>
> On Fri, Aug 8, 2025 at 3:02 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> &rst
>> iat=-1,-1,-1,-1,
>> r1=0, r2=90, r3=90, r4=180,
>> rk2 = 1000., rk3 = 1000.,
>>
>> IGR1(1)=747,IGR1(2)=746,IGR1(3)=744,IGR1(4)=750,IGR1(5)=753,IGR1(6)=754,
>> IGR1(7)=749,IGR1(8)=745,IGR1(9)=743,IGR1(10)=740,IGR1(11)=741,
>> IGR2(1)=735,IGR2(2)=755,IGR2(3)=757,IGR2(4)=738,IGR2(5)=737,
>> IGR3(1)=768,IGR3(2)=788,IGR3(3)=790,IGR3(4)=771,IGR3(5)=770,
>>
>> IGR4(1)=773,IGR4(2)=774,IGR4(3)=776,IGR4(4)=787,IGR4(5)=777,IGR4(6)=778,
>>
>> IGR4(7)=786,IGR4(8)=779,IGR4(9)=780,IGR4(10)=782,IGR4(11)=783,IGR4(12)=276,
>>
>> IGR4(13)=279,IGR4(14)=281,IGR4(15)=275,IGR4(16)=280,IGR4(17)=273,IGR4(18)=271,
>> IGR4(19)=270,
>> &end
>>
>> On Fri, Aug 8, 2025, 5:27 AM Gourav Das via AMBER <amber.ambermd.org>
>> wrote:
>>
>>> Greetings everyone!
>>>
>>>
>>>
>>> I am currently performing umbrella sampling simulation using AMBER20,
>>> and I
>>> need to define a pseudodihedral angle connecting centre of masses of four
>>> atom groups in the DISANG file.
>>>
>>>
>>>
>>> Could anyone kindly share a sample DISANG file or example input that
>>> demonstrates how to define such a pseudodihedral angle?
>>>
>>>
>>>
>>> For reference, I’ve included a standard DISANG file format for a dihedral
>>> restraint between four atoms:
>>>
>>>
>>>
>>> Harmonic restraints for 60 deg
>>>
>>> &rst
>>>
>>> iat=9,15,17,19,
>>>
>>> r1=-120.0, r2=60.0, r3=60.0, r4=240.0,
>>>
>>> rk2=200.0, rk3=200.0,
>>>
>>> /
>>>
>>>
>>>
>>> I’m specifically looking for an example where atom groups are used
>>> instead
>>> of individual atoms.
>>>
>>>
>>>
>>> Any guidance, suggestions, or example files would be greatly appreciated.
>>>
>>>
>>>
>>> Thank you!
>>>
>>>
>>> Gourav Das
>>>
>>> Research Scholar
>>>
>>> IIT Kharagpur
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Fri Aug 08 2025 - 05:30:03 PDT
